It's been nine years, but when I lived in Philly I often used SEPTA/NJ Transit to get up to NYC, and I thought it was great. It cost something like $14, instead of the $80 or so Amtrak would have, and it was really just as convenient - the two trains were coordinated so the connection was super-easy: if one was late for any reason, the other waited; they were just across the track from each other, etc.

The thought of taking the bus twice a day at rush hour is sort of horrifying to me - I would need to be REALLY broke to even consider that as a possibility. Plus, I think the point about being late for work is a really good one - not only is it awfully unlikely that with the 7 am bus you'd make it in the first place, but it also allows no room for roadway problems. It's not like accidents, lane closings, etc on the turnpike are uncommon, and the buses would always be caught in that, unlike the trains.

Personally, I'd go for either the sublet or the train.