Third KBED. It is the closes airport with the most heavy corporate traffic with rental cars on site. Figure on it taking roughly 15-30 minutes to get to the city if there is no traffic depending on which part you are headed to.
I flew in to KBED a couple years ago and used Signature, it was very expensive though I don't remember how much. Now I've moved to Boston and fly out of the same airfield with East Coast Aero Club (but they're not an FBO and don't offer parking AFAIK)
Jet Aviation is apparently a bit cheaper than Signature.
If you don't want to pay for a rental car there is a public bus, #76 (weekdays) or #62 (Saturday), which rns about every hour - check mbta.com. It will take you to Alewife subway station.
Other options would be Norwood (OWD) to the south and Beverly (BVY) to the north, both of which are near I-95 and Rte. 128. Both appear to have nearby MBTA commuter rail stations as well; North Beverly is two miles from BVY and Canton Junction is less than 3 miles from OWD.
I've never done what you're doing so I can't make any personal recommendations, but I would imagine that those two might be cheaper than BED. According to AirNav, 100LL is $7.03-$7.14 at BED, $5.98 at BVY, and $5.75 at OWD.
You're best bet would be to read reviews on AirNav or AOPA's online directory, call all three FBO's and inquire about fees/costs and transportation, and check out www.MBTA.com.