Where are you staying?
I agree about Boston Beer Works, I always go to the one on Canal St., right near north station. It's near the Banknorth Garden, and also not too far from the North End if you want to get some great italian food for dinner.
If you're closer to Allston you could go to Sunset Grill - they have a humongous selection of drafts and bottles, none that they make themselves but it's a great place and the pub grub is pretty good, too.
If you're down near the Prudential, I strongly recommend TC's Lounge. It's on Haviland Street. To find it, follow Boyleston Street to Mass Ave. Then turn on mass ave toward Berklee School of music. Haviland is a side street on the right, between the Dunkin Donuts and the Starbucks. TC's is just down from the corner, yellow sign. This is a place I've been going to since about 1990, and recently has been voted Boston's best dive bar. Cash only, so be prepared, but drinks are cheap, and you can head out to the other bars on Boyleston after you have a few cold ones at TC's.
Enjoy Boston! It's the best -- I lived away for about 14 years but moved back last summer and kind of wishing we never left!