Getting around Boston itself is fairly easy, but as Zelda points out, the suburbs are another matter, requiring a visit to the center of Boston to switch trains.
I just checked the other day, and a monthly pass to use the Amtrack to get from the station 7 miles from my house to Boston (about 60 miles away) would be US$270. Not bad. If I end up taking a job in Boston after I get my doctorate, I would seriously consider this option. I could use my iLiad during the ride.