Parking is $15 per day at the Port Authority's Long term lots, and $5.00 for each partial 8 hour period (e.g.,you pay $80. for 5 days and 6 hours) SEE-
http://www.panynj.gov/CommutingTravel/airports/html/ken_parking.html
It is very easy to get to the terminals from long term parking by elevated train with frequent service.
Competitors include Avistar and Airpark, which are a bit more expensive and give shuttle service to their lots.
Some airport hotels give parking deals if you stay at the hotel, and merit consideration if you have a very early flight.
JFK long term parking