This made me laugh. His story is a really good read.
The train that mncharity refers to is the much more reasonably priced NYC commuter rail, which does not reach Boston.
Ignoring the costs, I find the quality of life on the train to be far superior. No traffic, you can walk around, there are power outlets and the seats are pretty big.
For me, being able to work for 4.5 hours vs feeling carsick on a bus for similar or more time (I get nausea very easily when other people drive me), it was always worth it.
The other thing I would do is drive the car to an MTA stop and garage it for a couple of days while I took the commuter rail into town. Which option I took depended on ticket prices and the length of time I was staying.