Ditto Air & Space and Natural History (dinosaurs!). I just want to add that in the bottom level of the American History museum is the "Spark Lab" - a cool hands-on science area for kids. Plenty of educational toys and a long bar for the kids to sit at and participate in science experiments led by volunteers.
For toddlers to 5yo, I recommend the National Zoo (for obvious reasons) and the National Building Museum - which has a great play room
Building Zone