The short answer is, ALL OF THEM!! I've been lucky to visit many and enjoyed all of them. Here are some I recommend:

Hershey AACA (many exhibits are ongoing but they change the theme about every 6 months)
EMMR (Eastern Museum of Motorsports Racing)
Simeone Museum in Philly
Petersen in CA
Garlits
Petty
Wellborn
The Henry Ford (but it's not really automotive)
Walter P Chrysler (if it reopens)
Barber Motorsports Museum in Alabama (do that and Wellborn in one trip)
Keystone Antique Truck & Tractor Museum in VA
Swigert in Huntingdon, PA (OLD school place)
Ford Piquette Plant in Detroit (Ford's first plant)
GM Heritage Center
McCandless Museum once he opens it to the public

These are the ones that stand out the most to me.

Ed