From JFK gates follow signs to"ground transportation". Near baggage area follow signs to "airtrain". They will take you up escalators and moving walkways. Get on air train to Jamaica (there are two voices that alternate:Jamaica or Howard Beach). At end of line (Jamaica) which is about 7 minute ride from Jetblue terminal 5/6, everyone departs. You pay $5 to exit. There are machines to buy a metro card. You want to get a combined card with a train ticket on the Long Island Railroad to Penn Station. there are every helpful Metro workers nearby the machines who will help you. Get you tickets (if you will be using subways in NYC, add $20 or so to your metro card), go through exit turnstiles and head straight ahead to LIRR. Trains to Penn Station leave about every 20 min. Cost about $7 from Jamaica to PennStation. Takes 25 min to arrive. pennStation is at 32nd st and 7th Ave. Madison Square Garden sits on top of it.
Have fun.
To NYC west side