Boston Duck Tours are pretty fun and surprisingly interesting for history buffs -- you drive around the city and float along the Charles River in a WWII amphibious vehicle. The tour guides are really entertaining too.
Quincy Market is a good spot for lunch with lots of street performers.
Head over to Cambridge and check out the Harvard and MIT campuses.
The Holocaust memorial is very moving and absolutely worth checking out.
The aquarium and science museum are both world-class.
If you've never been to a classic old-style ball park, Fenway is awesome, particularly if you can get tickets to a Sox game.