I have done this. It's a long way to Tippera... oops, to Manhattan from Islip.
By public transportation: at the airport, catch a taxi from Islip to the Ronkonkoma stop on the LIRR, which would be about $4.00. The LIRR into the city from Ronkonkoma is about $12.00, I think - check www.mta.nyc.ny.us
By taxi: it's quite expensive, like $100. Ask the cab/car driver before getting in.
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I took that LIRR train earlier this year from Penn Station to Ronkonkoma a little bit after noon on a Sunday. It wasn't crowded and it took about an hour. I imagine it would be a nightmare during rush hour. The cab drivers were charging a fixed $5 rate to go from the train station to the airport. It's probably the same in reverse.
Take the shuttle bus or a taxi to the train station, then the LIRR (Long Island Rail Road) into Penn Station in Manhattan. It's not a fun ride, but if you are saving a ton flying into islip, who cares.
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Though it's a $5 flat fare from the LIRR to ISP, if he just takes a cab from the line at the airport to the train station, it will run between $12 and $15. If he calls and orders the cab, it's only $5. There's a phone in the airport that connects to Village Taxi, or he can call at 8003711058. Sunset also charges the flat $5 for a pickup, but I don't have their number handy. Colonial (6315897911)did run a shuttle for the same $5, theoretically connecting to all LIRR departures; I found them unreliable, but if it's there, he can grab it. Train to Penn is $9.50 peak, $6.50 offpeak. Except for rush hour express trains, trip is scheduled to take about 85 minutes, but it often takes longer. Good news is that since Ronkonkoma's the first stop, you can always get a seat.