Take Amtrak or Jersey Transit train from the Newark Airport Station (there's a light rail link from terminals to the station) to Penn Station-NY. Walk downstairs to the LIRR and take any train stopping at Jamaica (most do). Walk upstairs to the Air Train which will take you to all JFK terminals. Travel time depends on the train schedules. It's 20 minutes from Newark Airport station to Penn Station, 20 minutes from Penn Station to Jamaica and 10-15 minutes from Jamaica to JFK depending on which terminal. I'd allow two hours to play it safe.
Take Amtrak or Jersey