Quincy Market/ Faneuil Hall, USS Constitution, Bunker Hill Memorial, Fenway Park, Boston Common/Public Gardens, Freedom Trail, Chinatown, the Arboretum on Arborway, Downtown Crossing, etc. I could go on and on and on. You could walk around Boston, checking out Beacon Hill (expensive neighborhood) and Newbury Street's expensive shops. North End has Italian restaurants and such, and Chinatown, of course, has Asian restaurants. I might be able to give you some suggestions on those too. Most of what i have listed is in the Downtown area, with the exceptions of Fenway Park, the Arboretum, and the Bunker Hill/Constitution monuments, the latter being on the Cambridge side of the river. Even though you're visiting MIT (smartypants), go over to Harvard Square (more of a triangle, really). Lots of stuff there.
Oh, and i'm assuming you're renting a car. If you are, good luck. The Central Artery is hell to drive on. You can't turn on red and there's plenty of one way streets. Parking sucks, and in most residential areas, 7 PM - 7 AM is Residential Parking Permits Only, meaning you can't park there, and the meters turn off. If your hotel is in downtown, leave your car there and explore on foot. Everything is pretty easy to get to and within walking distance or can be reached by the T. Stay out of Roxbury or Mattapan.