You can get a monthly pass from NYP to BOS for $1700 or a ten-ride pass for $780. See here: http://tickets.amtrak.com/itd/amtrak/multiride

Taking into account travel time to and from the airports, plus time spent in security, you might be looking at longer than 3.5 hours.

Still, travel along the Northeast corridor would be a lot cheaper if those fares didn't have to subside ridiculous cross-country routes. A one-way ticket from New York to Los Angeles (changing trains in Chicago) costs $266 and takes 62 hours, not including the 5 hour layover. Why are these trains still running?