Keep in mind that Greyhound, Peter Pan, Yo! and Bolt are all owned or allied with the same company. Not that that will matter much, however.
I would also look at Lucky Star and Mega Bus. Consider Go Bus if leaving from Alewife or Newton is more convenient. Some of the 'Chinatown bus' companies have been shut down at some point (IIRC, Fung Wah has never reopened, Lucky Star has) for safety issues. Many of these companies have very low prices for a few seats on each bus. If you can get a $1 fare, then take that company.
Otherwise, it really doesn't matter. I would make the selection based on where they drop off in NYC.
Amtrak is certainly not on the level of good German trains, but it still might be worth the higher cost if you can get a good price.