I don't know about the best in the entire world, but the museum at Boeing Field in Seattle and the Evergreen Museum in McMinnville, Oregon are pretty good. The Spruce Goose is housed at the Evergreen Museum.
The Boeing Museum has a Concorde that you can walk through as well as a 707 Air Force One. The first 747 is there also. There is a very well done WWI and WWII section that you walk through, and it gives you the feeling that you are actually there with sounds and life sized figures, etc.
I have been told that there is a very good helicopter museum just south of San Francisco International which is on my list being a former rotor head myself.
