I took the Acela once. It is quite nice to leave from Penn Station and arriving at South Station in Boston. From there you can get directly to the Boston airport via the Silver Line. The Acela ride is just smooth. It goes right by the sea with nice views. I realy enjoyed it.

It is no hazzle to get to JFK it just takes time. From Manhattan its $45 by taxi and takes up to 60 minutes depending on the time of the day and where you start in Manhattan. Subway takes about 90 minutes but is way cheaper.