I see you've been to several aviation museums, but if you're ever anywhere near Ohio, may I suggest the Air Force museum? There are so many aircraft there that one can't see anywhere else, like the only remaining XB-70.

Some other personal favourites:

* Molson, Washington - it's a preserved ghost town, somewhat like Bodie, California, but one can go inside nearly all of the structures, and there is an actual museum set up in the three-story former town school.

* Not sure this counts, because The Met isn't a niche museum overall, but their Egyptian wing is the only place I've been to where one can walk through two more or less complete ancient Egyptian structures without going to Egypt.