About 40 minutes, but you can't get directly from teh Air train to manhattan - have to switch onto the subway. Check here -

I'm a NY'er and to be honest, unless you want a quick run into Manhattan for 3 - 4 hours, i don't see where there's much else to do. Bird watching sounds pretty impractical to me.

mind you, three to 4 hours in manhattan might be pretty cool to do, depending on the time of day.

http://gonyc.about.com/cs/airlinesairports/a/getto_jfk.htm