Depending on what time you're going, ground transportation from Manhattan to JFK can be a disaster. Just so's you know. (I'd assume the shuttle people would have a good handle on this, though.) If you do need a taxi, they're ubiquitous and flat-rated at $35+tolls.

I've always been happy with the A train (fast, cheap, and zero-hassle), but I can see why others (especially with lots of luggage) wouldn't want to deal.