I usually take the Regional on my own dime though last trip I got a deal on the return leg on Acela. The downside of Amtrak for me is that the Boston south suburban station is an hour drive in basically the wrong direction. But I hate hate driving into Manhattan.
Do you ever consider driving to New Haven and taking Metro North the rest of the way? IIRC it's as fast as Amtrak if you're on the Super Express train.