If you are looking to visit car museums in the USA, here is a list not to miss

here is a list of the top 10 in the world: http://www.edmunds.com/car-reviews/top-10/top-10-automobile-museums.html?articleid=122959 which completely agrees with http://smashingusa.com/12-definitely-worth-a-detour-car-museums-of-america/ and they agree that the Henry Ford, the National Corvette, and the Petersen are not to be missed and they surprised me with the Studebaker and the Natl. Auto museum in Reno (formerly the Harrah) http://www.automuseum.org/index.html

A top 10 list http://www.journeyetc.com/travel-guide/top-10-best-automobile-museums-to-visit-in-the-us/

I'll start in one corner of the USA and work towards California,

far North East is Maine and the Owls Head Transportation Museum: www.ohtm.org

two miles south of Rockland, eight miles south of Camden, and approximately 85 miles north of Portland. Cars, motorcycles, airplanes, bicycles, + research library and archives

The Boothbay Railway Village is in Southern Maine, south of Augusta, off hwy1 https://railwayvillage.org

in Massachusetts the Springfield Museums has the Gee Bee Aviation collection, the Indian Motorcycle museum, and car museums https://springfieldmuseums.org/about/museum-of-springfield-history/
And the Larz Anderson Museum https://larzanderson.org/

in New Britain, Connecticutt, is Papa's Dodge, a dealership and museum that has Wednesday cruise nights - burnout contests, and a classic car museum http://www.papasdodge.com/dream-cruise.htm
and Middlebury Connecticut is the Golden Age of Trucking Museum http://www.goldenagetruckmuseum.com/

Rhode Island has 2 new museums (2017)
The Newport Car Museum and and the Audrain
https://newportcarmuseum.org/
http://audrainautomuseum.org/

In New York is the Northeast Classic Car Museum http://www.classiccarmuseum.org/ in Norwich, half way between Syracuse and Albany
and the FDNY New York City Fire Dept museum in Manhattan's Soho district http://www.nycfiremuseum.org/
plus the Long Island Car and Carriage museum http://longislandmuseum.org/

the Glenn Curtiss Museum is south of Rochester https://glennhcurtissmuseum.org/ off I 390, and it has cars, planes, bicycles and motorcycles

in the Hudson Valley Rhinebeck Aerodrome https://oldrhinebeck.org/ of antique airplanes

on Long Island is the private BMW museum of Peter Nettesheim, but it's invitation only. 

In Newton New Jersey, there is an incredibly thorough snowmobile museum
 look for The Snowmobile Barn a passion of Mr. and Mrs. Klemm who operate D and K Transport
http://carzhunt.blogspot.com/2014/01/there-is-no-auto-museum-in-new-jersey-2.html


Pittsburgh's Bicycle Heaven Museum, https://www.bicycleheaven.org/

 the AACA in Hershey Pennsylvania http://www.aacamuseum.org/ ,
stop by Allentown and see http://www.americaonwheels.org/
or the Eastern Museum of Motor Racing http://www.emmr.org/ which Bangshift posted a gallery of http://bangshift.com/gallery/eastern-museum-of-motor-racing-gallery-2.html  you might try the Swigart in Huntingdon, PA http://www.swigartmuseum.com/index.html
Also the John Rich Museum http://www.jwrautomuseum.com/
and the Boyertown Museum/Penn state museum of transportation http://boyertownmuseum.org/

and the 3 Dog Garage museum  https://www.3dog.org/about-us is also in Boyertown
and the Eagles Mere Car and Airplane museum http://www.eaglesmereairmuseum.org/  and http://www.eaglesmereautomuseum.com/
The Simeone https://www.simeonemuseum.org/the-collection is in Philly

Wood Bros Museum in Stuart Virginia

In Cleveland Ohio, the Western Reserve Historical Society
Crawford Car and Aviation Museum
https://www.wrhs.org/research/crawford/

in Illinois,

 the Illinois Railway Museum, located 50 miles northwest of Chicago in Union, Illinois. 

The museum was founded in 1953 by 10 men who each contributed $100 to purchase Indiana Railroad 65, a recently retired interurban car that was on the verge of being scrapped. Since then, it has grown into the largest collection of historical railway equipment in the United States, and is owned and operated by volunteers.

https://www.irm.org/

The Museum of Science and Industry in Chicago, has trains, planes, cars, trucks, etc, even a submarine

https://www.msichicago.org/

In Chicago, by hwy 50 and 19, the https://klairmontkollections.com

the Gilmore in Michigan (doesn't open til May http://www.gilmorecarmuseum.org/ )
in Flint is the Sloan Museum which is focused on Buicks http://sloanlongway.org/automotive-collection/
and if you get into Michigan see the Motorsports Hall of Fame http://www.mshf.com/ ,
and the Detroit Historic Museum's collection http://www.detroithistorical.org/
plus the RE Oldsmobile Museum http://reoldsmuseum.org/
Benson Ford Research Center www.thehenryford.org/research/index.aspx
in Lansing near the capitol bldg is the RE Olds museum http://carnut1.blogspot.com/2010/12/car-blog-makes-visit-to-re-olds.html
and a must see is the Henry Ford in Dearborn http://www.thehenryford.org/museum/index.aspx
National Automotive History Collection   www.detroit.lib.mi.us/nahc/index.htm

the Ye Ole Carriage Shop in Spring Arbor, just outside of Jackson

and the Kalamazoo Aviation History Museum, also known as the Air Zoo https://www.airzoo.org

In Hartford Wisconsin http://wisconsinautomuseum.com/
and while in Wisconsin, you have to go see the Harley Museum http://www.harley-davidson.com/en_US/Content/Pages/HD_Museum/museum.html?locale=en_US&bmLocale=en_US
and at the far north tip of Wisconsin is the Duluth Railroad Museum http://lsrm.org/
And there is also a private museum of the Four Wheel Drive that were made in Clinton Wi
https://www.facebook.com/FWDSeagraveMuseum/
National Railroad Museum in Green Bay  https://nationalrrmuseum.org

The EAA Aviation museum in Oshkosh  https://www.eaa.org/eaa-museum

In Ohio, see the Packard in Dayton  http://www.wrsol.com/usatravelguide/2009/12/bestcarmuseums-americaspackardmuseum/ .. ..


and the Volo http://volocars.com/ in Illinois

and the Pontiac Oakland museum in Pontiac Ill  https://www.pontiacoaklandmuseum.org

in nearby Indiana is a Hudson museum Hostetler’s Hudson Auto Museum in Shipshewana
 thought to be the largest and most complete collection of Hudson, Essex, Terraplane, Railton, and Dover cars and trucks
Indiana: http://www.hostetlershudsons.com/
And while Indiana, see the Studebaker National Museum http://vft.org/Museums/StudebakerMuseum/StudebakerMuseum.html

and don't miss the RV MV Hall of Fame Museum in Elkhart

https://www.rvmhhalloffame.org/

 In Iowa  www.motormagic.info/museums.htm
National Motorcycle Museum in Anamosa http://www.nationalmcmuseum.org has about 800 motorcycles

The Union Pacific Railroad Museum https://www.uprrmuseum.org/uprrm/

Rails West Railroad Museum, in an 1899 railroad depot
https://www.thehistoricalsociety.org/

In Tennessee
In Nashville is the Lane Motor Museum
https://www.lanemotormuseum.org/
Greenville
The City Garage Car Museum
http://www.citygaragecarmuseum.com/#_=_
International Towing and Recovery Museum and Hall of Fame
http://internationaltowingmuseum.org/
And the Floyd Garrett Muscle Car Museum http://www.musclecarmuseum.com/ a little east of Knoxville

In Colonial Heights Virginia,
the Keystone Antique Truck and Tractor Museum
http://www.keystonetractorworks.com/

In North Carolina, be sure to visit the Richard Petty Museum
309 Branson Mill Rd., Randleman, NC
http://rpmuseum.com/

In South Carolina at the Darlington Speedway there is a stock car museum
http://www.darlingtonraceway.com/About-Us/Stock-Car-Museum.aspx

And the Wheels of Yesteryear collection museum of Paul Cummings 

in Myrtle Beach, South Carolina http://www.wheelsofyesteryearmb.com

The Wellborn Musclecar museum in Alexander City Alabama http://www.wellbornmusclecarmuseum.com/

In Tupelo Mississippi
http://www.tupeloautomuseum.com/index.php

In New Orleans is the Wedell Williams Aviation Museum
https://louisianastatemuseum.org/museum/wedell-williams-aviation-and-cypress-sawmill-museum
and the National WW2 Museum http://www.nww2m.com

In Arkansas, the former governor Winthrop Rockefeller donated some of his car collection to the Museum of Autos www.museumofautos.com  near Little Rock

 http://www.arkansas.com/blog/post/a-visit-to-the-museum-of-automobiles-in-morrilton/

In Oklahoma
The Hajek Motorsports Museum in Ames Oklahoma http://hajekmotorsports.com/about
 Phil Silva's Muscle Car Legends Museum http://www.pinemeadowcabins.com/muscle_car_museum.html

The Oklahoma Railway Museum  https://oklahomarailwaymuseum.org/

Oklahoma State Firefighters Museum  https://osfa.info/museum/welcome

the 45th Infantry Division Museum in Oklahoma City   https://www.okcadventure.com/places/45th-infantry-museum

The Microcar museum of Bruse Weiner in Madison Georgia (50 miles from Atlanta) http://www.microcarmuseum.com/ 

and the Punta Gorda muscle car in Florida http://www.musclecarcity.net/
Don Garlits Museum in Ocala http://www.garlits.com/
Sarasota has the 2nd oldest contiuously operated car museum; Sarasota Classic Car Museum http://www.sarasotacarmuseum.org/
In Palm Beach Florida is the Staluppi Museum http://www.carsofdreams.com/
and in Tallahassee the Automobile Museum even has a huge outboard collection and a Tucker
http://www.tacm.com/
and the Elliot in  Port St Lucie   https://elliottmuseum.org/
in Naples https://revsinstitute.org/

and the Farmall and International Harvester museum in Leesburg  https://stewsihstuff.com/museum-history

an absolute must is the Wheels Through Time in Maggie Valley North Carolina: http://www.wheelsthroughtime.com/

In Indiana
Mid America Motorworks, halfway between St Louis and Terre Haute on Hwy 57 http://www.mygaragemuseum.com/visitusmain.htm
and also the Kerstings Cycle Museum http://www.kerstingscycle.com/muse.html
the Indianapolis Speedway museum http://www.indianapolismotorspeedway.com/history/35204-Museum

While near St Louis,
the Dave Mungenast Classic Motorcycles Museum
http://www.classicmotorcyclesllc.com/
and the St Louis Museum of Transportation
http://transportmuseumassociation.org/index.htm

In Minnesota, 

the Greyhound Bus Museum https://greyhoundbusmuseum.org/

The only thing I've come across so far in Nebraska is the Union Pacific Museum in Omaha https://archive.org/stream/assassinationofunlinc#page/n53/mode/2up

and Speedy Bill's! It's the museum of American Speed in Lincoln http://www.museumofamericanspeed.com/default.dlp

http://www.hostetlershudsons.com/ In DeSoto Kansas is Grandpa's Garage and Body Shop http://www.classicaldrives.com/50226711/in_a_town_called_desoto_grandpas_garage_features_old_fords.php 

In North Dakota I've only learned of Bonanzaville, in Fargo 

It's a combination of the Eugene Dahl Car Museum, the Eagles Air Museum, and the Moen Tractor Museum https://www.bonanzaville.org/

In the middle of South Dakota is the Pioneer Auto museum http://www.pioneerautoshow.com/
Near Denver Colorado is Terry's private Nash/AMC museum that he welcomes car people to http://www.pnwnash.org/museum

While in Colorado see the Rocky Mountain Motorcycle Museum http://rocky-mountain-motorcycle-museum.blogspot.com/
and try to get Terry to show you his private museum of Nash autos near Denver http://www.nashcarclub.org/Rambler-Ranch/rambler-ranch.html
Near Pikes Peak is the Penrose Heritage Museum Group at the Broadmoor Hotel
and one part of that is the Pikes Peak Hillclimb Museum https://www.broadmoor.com/blog/july-2014/the-heritage-museum/
There is also the Forney Transportation Museum in Denver, https://www.forneymuseum.org
which has a Big Boy
the Denver Fire Fighters Museum

The Gateway Canyons Auto Museum  https://www.gatewaycanyons.com/gateway-auto-museum

 Texas
Museum of the American Railroad, just north of Dallas
http://www.museumoftheamericanrailroad.org/  https://www.forneymuseum.org/

Jack Sisemore's RV Museum in Amarillo https://www.rvmuseum.net/

The Haas Moto Museum and Sculpture Gallery in Dallas https://haasmotomuseum.com

Utah 
http://pricemuseumofspeed.org/ which is mostly pre ww2 rare cars, and has the Peerless Green Dragon, some Miller race cars and some Stutz

https://richardericksonfoundation.org is a 300 acre, 24 building, 50 year long collection in Wallsburg, between Provo and Park City on the 189

In New Mexico
Unser Family race car museum
Albuquerque http://www.unserracingmuseum.com/
and 40 miles from Albuquerque is the Lewis Antique Auto museum: http://www.classiccartravelguide.com/rust-desert-lewis-antique-auto-toy-museum/

In Pheonix Arizona is the
Penske Auto museum: http://www.penskeracingmuseum.com/
plus the http://www.hallofflame.org/ Firefighters National Hall of Fame and 90 pieces of firefighting apparatus
plus the  http://www.martinautomuseum.com/
and the Streetcar http://phoenixtrolley.com/
and a Harley and motorcycle museum http://www.buddystubbshd.com/custompage3.asp?pg=museum01
and the Open Wheel Racing Museum http://www.azracingmuseum.org/index.php/az-open-wheel-racing-museum
In Tucson is the Franklin Auto Museum http://franklinmuseum.org/
and the http://tucsonhistoricdepot.org train depot that's been restored
In Chandler is the http://www.azrymuseum.org/ train and railway museum
In Scottsdale is the http://www.scottsdaleinternationalautomuseum.com/

Here in So Cal...
The Nethercutt http://nethercuttcollection.org/Museum.aspx ,
Justice Brothers http://justicebrothers.com/pages/racing-museum/r&m_racingmuseum_main.htm ,
Mullin Museum in Ventura focusing on the Art Deco movement of auto design
http://www.mullinautomotivemuseum.com/the-museum.html
the Murphy is up by the Mullin, in Oxnard http://www.murphyautomuseum.org/
The Solvang Vintage Motorcycle http://www.motosolvang.com/

the Mike Malamut Auto Museum Foundation Collection is private collection / sorta museum, not open as a museum business, but open for events and car clubs http://malamutautomuseumfoundation.org/
Lyon Air Museum in Santa Ana http://www.lyonairmuseum.org/
Day Family Classic Car Museum off Iowa Avenue in Riverside
the Riverside International Auto Museum  http://www.riversideinternational.org/
the Marconi Museum in Tustin http://www.marconimuseum.org/
and you ought to see Galpin Ford's display of Roth customs, the Mysterion and Orbitron, plus the Ice Truck http://galpinautosports.com/2011/02/g-a-s-custom-classics-wow-the-crowds-at-the-grand-national-roadster-show/  and  http://www.bangshift.com/gallery/Galpin-Autosports-gallery.html
in El Segundo http://www.mercedes-benz-classic.com/content/classic/mpc/mpc_classic_website/en/mpc_home/mbc/home/museum/overview_museum.html

A little farther North near San Francisco,  in nearby Woodland is the Heidrick Antique Tractor and Hays Antique Truck Collections in one location, http://www.aghistory.org/ which might be the California Agricultural Museum  http://www.californiaagmuseum.org/

and in San Francisco the Academy of Art University museum http://www.academyautomuseum.org/
the Blackhawk in Danville, by San Fran http://www.blackhawkcollection.com/
and while in San Fran, see Brizios' shop!
Also, the Musee Mechanique on Fisherman's Wharf, Pier 45 http://museemecaniquesf.com/photos.php
and the Academy of Art University Museum in San Fran
http://www.academyautomuseum.org/

And somewhere about 25 miles East of San Fran is the Cobra Experience Museum only open 2 days a month in Martinez, https://www.cobraexperience.org

and the Talbott Motorcycle Museum near Monterey
http://www.mototalbott.com/

the Estrella Warbirds Museum near Paseo Robles, https://www.ewarbirds.org/index.html

https://rootsofmotivepower.com/
Motive Power Collection in the Mendocino County Museum, Willits, California. That's halfway between San Fran and the Oregon border

Roots of Motive Power is an all-volunteer organization founded in 1982 to preserve and restore steam- and diesel-powered equipment used in California’s North Coast logging industry from the 1850s to the present.

In Sacramento is the State Railroad Museum
http://www.csrmf.org/

and the California Automobile Museum
http://www.calautomuseum.org/

Between Sacramento and Reno is the Western Pacific Railway Museum

https://www.wplives.org/

then head over to Reno Nevada to the
Natl. Auto museum (formerly the Harrah)
 http://www.automuseum.org/index.html
and the Hays Truck Museum which is now part of the Natl Auto Museum
Up in Tacoma Washington, finally (I've been waiting 4 years) the LeMay museum is open http://www.lemaymuseum.org/

In Hood River Oregon, the Western Antique Aeroplane and Automobile Museum http://www.waaamuseum.org/

https://www.facebook.com/WAAAMuseum

Montana even has a museum
http://www.pcmaf.org/wordpress/museums-2/montana-auto-museum/

and in Fairbanks Alaska
the Fountainhead http://www.fountainheadmuseum.com/

Here's a list of museums by state: http://www.team.net/www/museums/us.html but it's 5 years old, and might not be 100% accurate anymore

Here is a link to a list of lots of US auto museums http://www.digital-librarian.com/car_museums.html

And for a look at some museums before you go, to make sure it's worth the trip: http://www.remarkablecars.com/main/aa-museums/car-museums.html

And Dennis has compiled an incredible list which he keeps updated, its more complete than mine will ever be! http://vft.org/vftmuseums.html