I fly for NJA out of MHT. It cost $385/yr for the crew lot which is walking distance to the terminal. You can take flightline to BOS terminal for $20? or so with your id. BOS parking is more, but I haven't flown out of there in 2 years. I did all the deals. You can park at a hotel off exit 45 from 93 for free and take Flightline for $10 each way and there is also Logan Express, or Paul's has a discount for cremembers. Going to the Logan office and get a parking at the chelsea lot for a month or by the book in the old days.
MHT has less flights. I say BOS for more options if you are a commuter. I'm sure glade I don't have that headache anymore!
The Delta crew parking lot in BOS. They have a guard there but they never actually get out of the box and check anything. Just wave and drive by. They have cars in that lot that have been there for years. One guy I flew with parked his camper there and he and his wife lived in the lot. I still can't believe she put up with that, great lady. The bus is there every 15 mins.
The lot is on Marginal Street almost on the corner of Willow Street near the Chelsea Street bridge. Good Luck.
Where are you trying to go? MHT is a lot easier to drive in and out of than BOS. There are fewer flights out of MHT, although I've always found Southwest to be pretty helpful when all else fails. They have something like 26 flights a day out of MHT. On the other hand, Delta is down to one RJ a day to Atlanta and 2 to CVG.