I'd forgo the car, too. For the rental fee + parking, you can easily get around via cab. The T is even less expensive and usually faster, but it depends, plus it can be a pain in the ass if you're going to Cambridge (Harvard is huge and is in many locations). Virgin arrives in Terminal E; Logan is actually a really easy airport once you get there , so I wouldn't anticipate any problems on arrival.

Hints on what you'd like to do or eat? Boston's not terribly large, but you do have a large amount of dining and entertainment options in a reasonably small and walking-accessible radius from your hotel. I'm sure there's something that will fit what you'd like, and I'd be happy to help.