Taking a taxi from the airport is convenient, but expensive (probably between $30 – $55).
Shuttle buses are a balance between convenience and cost-savings. There are several different shuttles that operate from the NYC airports. There’s not too much difference between their fares, but be sure to check each of their websites to see if they’re offering any special deals. Some at least give you a discount for booking your reservation online. The main complaint about the shuttles is that they can be very slow at getting you to your destination. It all depends on who else is on the shuttle, where everyone is going, and what the traffic conditions are like.
GO Airlink NYC. A door-to-door shared ride van service from the JFK, LaGuardia and Newark airports to Manhattan. They deliver passengers to their destinations starting with the closest first, so it could take a while to get to your hotel, depending on where it is and where the other passengers on the van need to go. The vans hold 11 passengers. They offer a 10% discount if you book online.
NYC Airporter. These shuttle buses leave the JFK and LaGuardia airports every 20 – 30 minutes. The shuttles have free wifi. They take you to Grand Central Station, Penn Station, the Port Authority Bus Terminal, or Bryant Park. You then have the option of taking one of their complementary shuttles from Bryant Park to a hotel located between 23rd and 63rd street, or taking a cab or other form of transportation to your hotel.
The least expensive way to go (and maybe the quickest) is to take public transit. You’ll save money, but you’ll have to make some transfers between buses and trains. This option is probably best if you’re traveling light.
And here’s public transit connection information from MTA.
Here’s a good thread at TripAdvisor where different options for getting to and from JFK are discussed.