I didn't mean, "Do you accept payment via EZ-Pass?" I meant, "Do you take your EZ-Pass (Fast Lane in MA) or M-Tag with you when you travel?" Most of northeast is EZ-Passified so you should be able to breeze through the Mass Pike tolls using your transponder from Maryland. (I assume from your Profile that you are based in MD.) Depending on when you plan to drive, the cash lanes can get pretty backed up while EZ-Passers / Fast-Laners just zip on through.
I agree with the ease of the 84-90 (Mass Pike) / 90 minute suggestion. Bostonguy suggested that you consider flying in and out from the same place and do a round-trip car rental, too. I have no idea what the one-way drop off fees are for rentals but Boston is not car-friendly. Be sure to check that out ahead of time to avoid sticker shock.