There are a lot of ways (from BOS at least) to get to NYC. There is the greyhound bus (south station to port authority) for $30 each way, of the china town bus (BOS china town to NYC china town) for $20 each way. You also get kung-fu movies on the china town bus

A much more relaxing way is to take the acela, but that is more expensive.

US Air has hourly shuttles to LGA but that can be $100 each way + the $30 cab between LGA and JFK. Or AA runs RJ's between BOS and JFK. DL flys that route as well, but i haven't taken them before.