In Boston there is a trail you can walk around, I recommend that, as part of it you visit the tea party location and there is an old British ship you can look round, which is quite good and the American sailors give you verbal abuse for being British as part of the experience. The trail is short enough for kids.
The highlight for us was a tour of the town hall (it is just down the street from the Cheers pub), which sounds odd but the tour guides were lovely and interesting and took us to lunch afterwards in their staff canteen so they could talk to us about England. The people we met there were so nice. We also got bought dinner by some Americans who were in Boston on business and bored and who had passed the time with us.
I thought the Children's museum was ok. There was a science/natural history museum to the north of the city we got the subway out to and that was ok too. Only ok though, I think we are spoilt here with our museums. I found some of it a bit dated.
The aquarium and bus tours were good.
I though Harvard was a bit boring to be honest, just the same as any old Uni here. You couldn't go in anywhere to have a nosy. We visited MIT which was much more interesting, they had a visitor centre that outlined stupid things students had done over the years, which was entertaining. We then wondered into one of the buildings and had lunch and watched student life and wished we could do it all again. I don't know if there will be more security there these days.
Boston is a good city to just kind of hang around in. Very pleasant. Writing this is making me want to go back!
Washington was good too, but felt much more like a city you need to be careful in.
Visit to FBI building (Or was it CIA? can't remember) was great, you can watch them fire a gun and see inside the labs and I think it was free. The museums in Washington were fab and all close together. All free too. Maybe go to museums in Washington instead of Boston? You can go up a tower thing near the White House and that was good too. The White House was fab, not sure if you get as much access as you used to. Good to see all the places you see on the TV. You can do a tour of the Senate and House of Representatives and that was worthwhile.
The Holocaust Memorial Museum is something special but I wouldn't go there with kids under 12. Some exhibts are labelled as potentially upsetting but the whole thing is very intense and if you go you'll need some time to relax and reflect afterwards.