Two things:
- The list of gates in ParkMe doesn't list all gates at all terminals, but only those were an assisted parking system exists, which for JFK it's the SafeDock type 3
- For several reasons, due to naming limitation in the FSX AFCAD engine (it's not possible to have something like "Terminal 1 Gate A1 to Axxx", "Terminal 1 Gate B1 to Bxxx" ), the assignment in the AFCAD, which are the assignments known to the ATC and used by the FSX World "Go To Airport" menu, don't match with real world, but use a different naming convention.
The ParkMe menu can also be used to see how the designation in the AFCAD are matched to real-world parking designations, but only for terminals supported by ParkMe.
For the rest of the airport, the best option would be using the free ADE (Airport Design Editor) to open the KFJK AFCAD, and have a look at the parking designations, perhaps printing a map of them.