L.R.
Here are some ideas. Thoughts on why the Spy Museum and Newseum are not for younger kids are at the end.
At the D.C. museums, there are hidden things just for kids but you have to know they're there! Have you tried: The "Spark Lab" at the American History Museum? This is a special room with stuff to build, adults helping kids do experiments, etc. Kids love it. It has specific hours it's open and they're not all the same as the museum hours so check first. Also at American History is "Invention at Play" for kids, a hands-on invention-themed area very close to the Spark Lab. The Natural History museum also has a kids' room, hidden away so you have to ask for it, that is a quiet place for lots of hands-on stuff - kids can pull out boxes of fossils etc. and look at things under microscopes and so on. Again, hours are limited and it's not open every hour that the museum is, so check its hours before you go.
Baltimore has a wonderful science museum with tons of dinosaur displays and last time we were there, kids could help "dig" a dinosaur. The museum is near the Inner Harbor area and very kid-friendly.
In Baltimore, the Walters art museum has kids' packs for exploring its collections (these direct kids to certain artworks and give them activities to do); I believe the kids' packs are available on weekends between certain hours--as always: Check first! They do have a limited number of packs so get there when they open if you do this.
You say you've been to "the aquarium" but which one? Both? Have you tried the "National Aquarium" that's in the basement of the Commerce Dept. building? It's very small but therefore doable and has some cool things-- the world's friendliest octopus, for one. And it's much less crazed than the overcrowded but admittedly terrific aquarium in Baltimore.
If you want something really special, see if Imagination Stage in Bethesda has a show on that weekend. It's professional kids' theatre -- adult performers specializing in shows for kids. Fantastic stage, fantastic shows, well worth the short drive (and there is a huge, super cheap garage right next to the theatre). Or see if the Smithsonian's own kids' theatre (in its Ripley Building basement) has a show on. Another fun place is Glen Echo Park's puppet theatre or the Adventure Theatre for kids, also at Glen Echo Park. Theatre is the best!
I know others suggested them, but I think the Spy Museum and Newseum both are not really appropriate for kids the ages of your kids, especially the two younger ones. I've been to both several times, but with my daughter who is 11.The younger kids just will not understand most of what's being talked about at the Spy Museum (its promotional materials make it look cool and kid-friendly but its exhibits mostly are about real and serious spy stuff-- but do kids really get the Cold War, for instance?) My daughter loves it but she is much older than your kids....The Newseum I definitely would not recommend for kids until they are maybe 9 and up at least; there are a lot of current-events history displays that are beyond younger kids, and some exhibits feature news photography that can be graphically violent. Both the Newseum and the Spy Museum are expensive, too, so it's a waste if you pay a lot for a family of five and the younger ones get bored and then you adults can't enjoy the exhibits either. Both museums are great but not for younger kids.