Just an FYI, as I assume that this doesn't apply to the original post (which seemed to imply that "nice" transport is required.)

Taxis from JFK to anywhere in Manhattan are a flat rate of $35 plus tolls and tip. So, anything you pay a car service above and beyond is for the knowledge that you don't have to wait in the taxi line- unless you make special requests or use a high-end limo service, there's no guarantee that you'll be travelling in any more style/comfort than regular yellow cab.

I used to arrange livery cab pick-ups ahead of time at JFK, because you never know when the taxi line was going to be an hour long.

However, since 9/11 I just take cabs- I can't think of one time since where I've had to wait for a cab longer than it would have taken to meet up with a driver from a car service.