Actually, the MIT Museum is pretty cool. There's a holography display and a display devoted to hacks (for instance, they have the fake campus police car that was put on top of the Great Dome a few years ago).
Legal Sea Foods is, IMO, overrated. You might want to try them at lunchtime for a bowl of clam chowdah, though.
Go to the Boston Public Garden and take a walk, it's very nice. Take a swan boat ride if they're still running them (although I think they stop on Labor Day).
There's also the Freedom Trail.
There are a bunch of nice shops and restaurants along Newbury and Boylston streets. (But bring $$$)
Have fun!
