Memorial Day weekend is hugely busy, what with the memorial events and Rolling Thunder (about ½ million or more motorcyclists arrive for memorial events and a ride through D.C. Many people stay a few days after that weekend, too, as it's the start of the summer tourist season.
Lines into museums really depend on what kind of special event that particular museum is sponsoring. The year Air & Space featured the bridge of the TV starship Enterprise, there wasn't a day throughout that exhibition that the lines weren't extremely long.
You really should do some homework into what special exhibitions there will be at the museums you want to visit. Could be a big clue into how long the lines will be.
Good luck and enjoy your visit.