Also saw this article and thought it was pretty cool. I've only been to the Smithsonian and Steven F. Udvar-Hazy Center and both are incredible. I feel like the National Naval Aviation Museum in Pensacola is worthy of the list and I've always wanted to see Red Bull Hangar-7.
http://www.cnn.com/2014/02/07/travel/best-aviation-museums/index.html?hpt=hp_c4
http://www.cnn.com/2014/02/07/travel/best-aviation-museums/index.html?hpt=hp_c4