The other Bostonians and ex-Bostonians here pretty much have you covered.
I second the recommendation that you not rent a car. Get a taxi or airport shuttle into Boston. They don't call Massachusetts drivers "Massholes" for nothing.
I had a car when I lived there, and I still took the T whenever possible.
Logan Airport - DeltAlum, you are right on. I used to fly out of Logan every week, and with the Big Dig, every week the approach was slightly different... the cab driver got lost on more than one occasion! The Ted Williams Tunnel helps a little with the traffic flow.
Bars - If you like beer, try the Sunset Grill & Tap. 110 beers on tap
Also, try John Harvard's in Harvard Square.
Weather - You'll want a sweater. In New England, the rule is "If you don't like the weather, wait a minute"
so be prepared for anything.
Enjoy your visit!