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From JFK take the Air Train to Train Terminal – Jamaica / then take the train to Penn Station.
Only takes around 30 mins and is fairly easy.
You need to buy a ticket at the end of the air train to get into the station, then either download the LIRR app to buy tickets into Penn Station or you can buy from the ticket booth.
It’s really easy and I find it quicker and cheaper than a cab or Uber.