As a person who travels via airplane very frequently, I feel I am qualified to answer this question.
I tend to look at the airports according to the ease of travel to/from them. Here are the options:
There is a subway (the A train) that goes directly from JFK to anywhere in the NYC area accessible by subway. This also means that you can get to/from the airport for $1.50. The ride to Midtown is about one hour.
Since JFK is pretty far from everything, the cab ride to Manhattan is a fixed rate of $30. It takes about 30-45 minutes.
LaGuardia is the closest to Manhattan, but the transportation to/from is pretty weak. There is a shuttle that goes from LaGuardia to Grand Central that costs $12 round trip. Cab fares are metered so they vary - from LaGuardia to my work (Midtown) a cab costs $20. Both methods take about 20 minutes.
Newark is BY FAR the worst airport if you are traveling to NYC. Flights to it may be cheaper, but you will end up paying a ton more in time and transportation costs. A cab costs a minimum of $30 - gypsy cabs and car services are around the same price. It can take from 45 minutes to over an hour depending on tunnel and turnpike traffic.
The public transportation is HORRIBLE. The buses (I think they’re like $12 round trip) take the passengers to Port Authority. It can take about 2 hours to get from Newark to Manhattan on the bus.
None of the above include tips and tolls. If you know your way around, you can avoid tolls. If you are traveling from Newark, it is imperative to tell the driver to take Routes 1/9 north instead of the Turnpike - you’ll save several dollars and a lot of time stuck in traffic. If you fly into LaGuardia, have the driver take the Queensboro or Williamsburg bridge into Manhattan - free. If you’re coming from JFK, have the driver take the Brooklyn or Manhattan bridges in - free. The tunnels cost $3.50 into Manhattan.
If you decide to rent a car, it’s cheapest through JFK.
Another option for travel to/from the airport is the one I use: the car service. If I don’t have vouchers from work, I just pay the $20. It’s nice because they pick you up at your home, take you directly to your ticketing counter and are generally pleasant. Unfortunetly, they drive like hell.
Depending on how much stuff I’m carrying, how much money I want to spend and how much time I have, I either choose LaGuardia or JFK.
Hope this helps.
Melanie