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 suprised me with the Studebaker and the Natl. Auto museum in Reno (formerly the Harrah).
Some others: the Gilmore in Michigan (doesn't open til May http://www.gilmorecarmuseum.org )
and if you get into Michigan see the Motorsports Hall of Fame http://www.mshf.com/ ,
the AACA in Hershey Pennsylvania http://www.aacamuseum.org/ ,
and if you got to Penn stop by Allentown and see http://www.americaonwheels.org/
you might try the Swigart in Huntingdon, PA http://www.swigartmuseum.com/index.html
and the Punta Gorda muscle car in Florida, the Indianapolis Speedway museum, and a must is Speedy Bill's!
The Lane museum is quirky and full of micro cars, it's in Nashville, and the Crawford in Cleveland are both in this top 10 list http://www.journeyetc.com/travel-guide/top-10-best-automobile-museums-to-visit-in-the-us/ While in the neighborhood of Illinois / Ohio, see the Packard in Dayton Ohio http://www.wrsol.com/usatravelguide/2009/12/bestcarmuseums-americaspackardmuseum/ .. ..
Ya gotta see Speedy Bill's! It's the museum of American Speed http://www.museumofamericanspeed.com/default.dlp
In Pheonix Arizona is the Penske Auto museum: http://www.automotto.org/entry/jaunt-across-the-car-museums-of-america/
Here in So Cal, which you'll probably not consider during the trip, but sometime afterward... I still haven't gotten to these myself: The Nethercutt, Justice Brothers, Blackhawk, and you ought to see Galpin Ford's display
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