We enjoyed the duck boat tour. A little cheesy, and touristy, but it was pretty fun and interesting.
http://www.bostonducktours.com/ Tickets sell out way ahead of time.
Hopefully the Sox are in town. Nothing compares to the environment inside and outside fenway during a game.
Walking around Harvard is cool.
Walking the Freedom trail is pretty interesting.
Newbury street has some cool shops and good outdoor eating.