Don't forget Harvard Square! There's a TON to do down there!
Down Mass Ave (towards the Harvard Bookstore etc.) there's a chinese restaurant called Hong Kong...upstairs above this restaurant is a small theater w/ a comedy show almost every night. It's called The Comedy Studio (I believe) and it's only $8! I just went 2 weeks ago, it was a great time. It's only 2hrs long (8pm-10pm about) so you still have time to do other stuff.
And of course, check out the theater district. There's always cool stuff down there. Mon Sept. 29, The Wang Center is showing "Breakfast at Tiffany's" for FREE!
I second the notion of the Isabella Stuart Gardener Museum. That place is so beautiful!
For eats: almost anywhere in the North End is great, and the area in/around Fanieul Hall/Quincy Market.
Enjoy your stay in the city. I LOVE BOSTON!
