New York is one of my least favorite destinations as far as airports at least. There are plenty of choices, but never one that looks appealing. Pricing, distance to destination, connections, and other issues combine to make for a miserable experience.
LaGuardia Airport
LGA is usually your best option because it is a quick trip to Queens and Manhattan with lots of flights 1,000 miles and shorter. The terminal facilities can be better, it’s almost impossible to find a seat with a view and there is nothing worth eating post security. You also have to take the M60 bus to catch a train into the city. The FAA imposes antiquated restrictions on flight distances, so rule out direct from the west coast. Further, there is a curfew and you’ll be landing at JFK if you miss it. There are two runways and lots of traffic, so be prepared for a long taxi during rush hour or if there is weather.
Newark Airport
Newark isn’t that far from Manhattan, but going to New Jersey never sounds appealing. It’s a $14 train ride from the airport to Penn Station and from there the subway system awaits. Not all that inconvenient really. The terminals are spacious with good views, ample seating, and a wide array of food options. Delays aren’t that bad either. It does take about 2 hours to get from Queens to your gate. Best option for connecting.
It’s like Heathrow, every flag carrier flies there and there is no simple connection. Delta and JetBlue own JFK on the domestic flights. No one carrier owns international, but Delta is strongest. Getting into Manhattan or joining the subway network can be done by rail. However connecting to LGA is a pain as there is no direct way to do it. The airport itself is pleasant and has great plane spotting.
Long Island MacArthur Airport
US Airways props to PHL and Southwest are your two options. It is out in Islip and a good option if you are going to Long Island. There’s a train to get you into NYC, but it’s a long trip. Southwest has been scaling back their operations as they grow in LGA and EWR. I don’t think they will abandon this airport, but it is part of the retired Southwest model of driving to a secondary airport for lower fares and doesn’t fit with their new priorities.