The quickest and easiest way to get to the piers is by taxi. There will be plenty waiting outside the airport terminal. If you are sailing out of Manhattan, the fare from JFK will be a flat $45, plus tip and tolls (if applicable). If you are sailing out of Brooklyn/Red Hook, the fare will be metered, but having not sailed from there myself, I do not know the approximate fare.
From JFK to the Manhattan piers should take anywhere from 45 minutes to an hour depending upon traffic. Also, remember to check your documents for the latest time you can check in, as it may be as early as 3:00 or 3:30.