Fuck driving, take the T where you need to go. Its 1.25 for a ride, and you can get a card with any value you want. The T, while never punctual, takes you pretty much anywhere you need to go in Boston. Definitely tour Fenway, and while you're in that area check out Boston Beer Works, its a great place to grab a bite, watch some sports, and have a good beer.
If you get sick of eating at any of the 8 trillion Legal Seafoods, there's myriad good restaurants on Newbury Street, which is a place you should check out anyways. Good shopping, nice place to walk around, and Sonsie is a good restaurant.
If you feel like going out and dropping $50 for some amazing Port wine and dessert, check out Todd English's dessert restaurant Finale. There's one in Park Plaza, one in Harvard Square, and one at Coolidge Corner.
If you're looking for good bars, there's a number of good ones around Coolidge Corner, as well. Go to Chinatown (Boylston St. stop on the Green Line on the T) if you want to have some legit Chinese food and do some sakebombs.
If you have time, do NOT miss the Museum of Fine Arts, which has a stop named after it on the E-Green line (outbound). MFA is one of the most impressive collections in the world, and its the kind of thing you could spend a whole day in.
Forget about the Boston Duck tours; $29 tourist trap.
The Science Museum is pretty cool, I think they still have the Body Works exhibit (real human cadavers on display).
If you're into cigars or wine, be sure to check out Churchill's Cigar Lounge at David P. Ehrlich Co, which is the second-oldest cigar store in the U.S. (1868). With a walk-in humidor, you can get all sorts of cigars and then plop down in an infinitely comfortable leather sofa with a nice Merlot and watch sports.
The Boston Aquarium is usually cool, and its got a ridiculously huge tank in the center, but probably not worth the price of admission this time of year.
The prudential center is definitely a good way to be tempted to drop hundreds of dollars on shit you and whatever lady may be accompanying you don't need; Gucci, Lacoste, Chanel, Louis Vuitton. All there.
I'm actually in CT right now, so you won't get to see me. But good luck.