The shuttle is really quite easy to use, because it is shared and everyone is travelling to different destinations it can take a little longer than a taxi. The taxis have a flat fare from JFK to Manhattan of US$45 dollars (well it was when I went in March). Given that there are 2 of you and for ease I would suggest getting a cab into Manhattan - you can always get the shuttle bus to take you back to the airport when you leave.
The shuttle is really quite