I was not in town for much more than 24 hours.  The downtown hotels were full, so I stayed in a Holiday Inn that was about three miles away.  Rooms were cheaper farther away from downtown, but I had still never before paid so much for a room and gotten so little.  A three mile train ride seemed to take about 20 minutes.  The trains are not terribly fast if you are used to a mile being equal to a minute.  You can buy a general purpose "Charlie Card" at the train stations that will last several days for the price of one cab ride.  Personally, I would not want to drive a car since I don't know the area not to mention where to park. 

I'd be inclined to try to stay somewhere close to most of the things you want to see and also close to a train station for sure.  You can have some good lobster at a mom and pop resteraunt for far less than it would have cost back home.

Here is a link to a train map: http://www.mbta.com/schedules_and_maps/subway/