When it comes to domestic flights, Philadelphia is usually cheaper then any of the New York Airports. I have family in NY and family that often flies in to visit them from the west coast and it has always consistently been that way. This is not the case however when it comes to international flights. In fact its the opposite. As a result of this, I know many people around here (PA) that go up and leave out of Newark, JFK, or Laguardia when flying overseas. When they go it is almost always by train and they have told me the details many times but I never really paid that much attention since whenever I go to NY I drive. So if your looking for a balance between cost, time, & convenience, I would suggest flying into Philadelphia and taking the train up. I think you take the airport line up to Trenton NJ and then can get a train into the city. If you want to take the bus route, I'm sure its possible. Everytime I'm on the NJ Turnpike, the bolt buses are everywhere. I travel to NY quite often and it takes a little over 2 hours by car. Let me know when your going and I'll see if I'm headed that way. At least you'd get a free ride one way.
If you want to consider additional airports, I believe you could get a similar setup of service through Balitmore MD, Providence RI, and Boston MA., although they are not as close.