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We are in the preliminary phase of adding this to our NYC trip next Fall. Here are some questions:
1) We understand we can take the LI Rail to Greenport. Are there rental car agencies in that vicinity?
2) Does anyone know if we can take the LI Railroad to JFK? If so, time it takes?
3) Any favorite places to stay? We are looking @ Harbor Knoll and The North Fork Table and Inn.
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Long Island North Fork
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The LIRR does not go to JFK. But you can take the LIRR to the Jamaica station and there get the Air Train ($5) which goes right to JFK.
I don't know the North Fork well - so I would google for car rentals.
But - depending on where you're coming from you might want to rent a car from there and return to JFK. In the fall the traffic out to the far island is nothing like as awful as it is in the summer - and a car would give you the ability to stop and see things on the way (Teddy Roosevelt's house among many other things).
There are very few trains that go all the way to Greenport--perhaps two or three all day.
If you don't want to drive the entire distance from NYC to the North Fork, the best option might be to take the train to Ronkonkoma, for which the LIRR has hourly service or better for most times of day and takes about 1.5 hours from Penn Station. Since the Ronkonkoma station is just minutes from Islip MacArthur Airport, I'm sure you'll find car rental options nearby.
The drive from Ronkonkoma to Greenport would be about an hour, though you would reach the western end of the North Fork in about 30 minutes.
The trip back from Ronkonkoma to Jamaica is about an hour. As nytraveler mentioned, there you can transfer to the AirTrain and be at JFK a few minutes later.
You can also use the Hamptonjitney.com to get to Greenport from NYC and back to JFK using the airport connection in Queens. It's likely more frequent than the train. http://www.hamptonjitney.com/PDFS/NF_20090924.pdf I see an Enterprise car rental in Riverhead (also a Jitney stop) and a Hertz in Cutchogue. Jedediah Hawkins is a beautiful inn and restaurant although I think their restaurant has suffered since the change of chef.
I live on the North Fork of Long Island and the Fall is certainly a beautiful time to visit. Just keep in mind the weekends in October (not sure what month you are planning to visit) can be crowded with pumpkin picking families.
I second the idea of using the Hampton jitney to Greenport. Why not rent a car and drive out to Greenport? It's a straight drive on the Long Island Expressway to the end and then a scenic drive on Sound Avenue. I would avoid early weekday mornings and evenings, instead driving out mid day or better yet, early Saturday morning.
I loved North fork Table and Inn, Claudio's on the water in Greenport for a casual meal. I've never been to Vine in Greenport but it's a wine bar with a nice menu and I've heard good things. Jamesport Manor Inn restaurant is good as well.
I've never stayed at any of the hotels in Greenport but passed by a beautiful place called the Bartlett house inn. If you are looking for a motel type place right on the water, you could try Soundview Inn, and for a spa-like getaway the Greenporter. Again, I've never stayed at any of these places, just drove by so you might want to check tripadvisor or this board for more information.
I had my best meal on the North Fork at North Fork Table a few weeks ago. Highly recommended. Another place you might check out is Shinn:, owned by a winemaking couple who used to own a very popular NYC restaurant, HOME:
http://www.theinn.recipesfromhome.com/
You also might want to check out these two restaurants in Mattituck; both are far superior to Claudio's in my opinion:
http://www.lovelanekitchen.com/
http://www.amanorestaurant.com/
In Greenport itself, the best food is probably at The Frisky Oyster restaurant; they also serve food at their new wine bar. I have not yet been to the wine bar:
http://www.thefriskyoyster.com/