So many options, it's tough to pick. I'd factor in what their interests are.
We recently did Mount Vernon and although some of it is closed off due to restoration, it was a great place to "set the scene" for much of what they will see.
The Metro is great. You can put SmarTrip cards on your phones/smart watches.
If you want to introduce them to the Holocaust without overloading them, the Holocaust museum has an exhibit that you can walk through that is outside the ticketed area (but still inside the museum). It walks you through a boy's life as the nazis take over. You can go through it without ever entering the main exhibits.
The American Indian Museum is less traveled, so if you need to escape some crowds or fill some time, it's a good place and their cafe is surprisingly good...expensive, but that is everything in DC.
Take advantages of bathrooms wherever you can. Lots of public restrooms are behind the security entrances and long lines, which are everywhere.
Make sure the kiddos have comfortable broken in shoes. My son packed a new pair of shoes and paid the price.
The pandas at the zoo are pretty cool to visit.
I found the American History Museum to be more cultural history and more interesting for me (seeing things from my youth) than it was for my son.
The Archives was great, but didn't require tons of time.
The Library of Congress (across from the Capitol) is beautiful inside and imparts a greater appreciation of literature...if any of your kids are big readers, it's worth a quick walk through. There is also a tunnel which connects it with the Capitol...underground and air conditioning is good thing in the summer.
Th senator and representative offices are in buildings around the capitol. If you reach out to them you might score some special Capitol tours up into the dome or have the opportunity to meet with them.
The Bureau of Engraving tour - it was alright, but I wouldn't recommend it to anyone there for just a few days.
Have a great trip!