Yes, the Freer is one of the best *least crowded* of the museums, and the metro station is right in front of it. We also love the collection at the National Portrait Gallery, there are some magnificent portraits of our founding fathers, etc., for your history buffs. We have been in on Saturdays and just walked in on kids' craft programs which have been really fun/free.
Also, I just noticed this, which is pretty funny:
http://www.npg.si.edu/exhibit/colbert.htm

Last but not least, ds8 loves the National Gallery's outdoor sculpture garden. It is a great place to explore and flop around on the grass after a day of walking.
For those who don't know it, all the Smithsonian museums are free to enter.