I will arrive in JFK and then take a train (Acela) to Boston.
How far is the station and which is the best way to get there?
Thanks.

Maggie - you've got to do some homework here. You've first got to get from JFK to Penn Station by bus, bus to subway, or taxi. The "best," ie. most convenient, way is probably taxi, but it'll cost ya.

The cheapest way is to take the free shuttle bus to the A train (subway) which is just a short distance away. You buy a $1.50 Metrocard or token at the station that will let you get to the platform. I don't think the trains run very often, maybe once every 20 minutes or so (there are no real "set" schedules). It's about an hour ride to Penn Station/33rd Street, where you can go to the Amtrak counter to buy your tix to Boston.

If you were to take a taxi or bus, it would take over an hour, also. Traffic by JFK is horrendous!

Any way to switch your flight into Newark? The new airtrain link at Newark is a monorail that takes you to a train station where you can pick up the Amtrak trains, right on Newark Airport property

Anyway to change your flight to Boston?

Why are you taking Acela if you're already at JFK? I would take a flight directly to BOS since you're already at the airport. The only selling point of Acela is if you're already in the city center.