I agree -- the Westin and the Marriott are the two best in Boston without busting up your wallet too bad.
I'm pretty sure there's a Sheraton or a Hilton in Newton a few miles off campus if you're not in the mood to be right in the middle of the city.
As for the T, make sure the hotel you stay at is close to the green line. I don't care what anyone says, at times switching trains can be a huge pain in the ass, especially if its a busy time of day.
I'm an undergrad at BC, and I've lived in or near Boston my whole life. When the time gets closer, PM me if you need some suggestions on going out in both Chestnut Hill and Boston.