Coming in from the airport, why not just take a cab? The fares into Manhattan are fixed at $45 plus tolls and tip and it's easy enough to get one at one of the taxi stands at JFK.

I've used both 7777 and 6666 and they've both been fine for what I needed. I've never had an airport pickup, only in the other direction, but they've always shown up on time, even when I'm leaving at 4AM for a 6AM flight.