The most flexible route into the city from JFK is a taxi, although the wait for one can be long when many flights arrive simultaneously.
Cab fare runs a flat $45 to anywhere in Manhattan, not including tolls (up to $4) or tips (15-20% depending on the level of service). Follow signs "Ground Transportation" and "Taxi" to the taxi line outside the arrivals area and look for the taxi dispatcher.
Taxis to points other than Manhattan and taxis to the airport from anywhere use the meter.
During peak periods, you may have to wait up to 30 minutes for a taxi. Note that the arrivals terminals are filled with drivers hawking illegal livery rides at grossly inflated prices that prey on newly arrived tourists, so beware. If you feel comfortable doing so, you can sometimes bargain with the touts to get down to $35-40. (This saves the wait in the taxi line.)
Taxis in New York City
Real NYC taxis are yellow, have a metal seal on the hood ("medallion"), a light with a taxi number on the roof, a meter for billing, stickers on the windshield for various licenses, special taxi license plates, and a divider in the car. If only the medallion number on the roof is lit, the taxi is available for hire. If the medallion number on the roof is not lit or the off-duty sign on the roof is lit, the taxi is not available for hire. However, sometimes the taxi will stop for you even if the off-duty sign is lit, usually if you are going in the same direction as the taxi driver to turn the cab in after his shift, so if you are desperate, it's worth a try to hail it. The meter starts at $2.50, and then $.40 for each 1/5 mile afterwards. There is a night surcharge of $0.50 (8pm to 6am) and a rush hour surcharge of $1.00 (4pm-8pm M-F). A tip of 10-20% is expected and passengers must pay all tolls. "Yellow cabs" cruise in most of Manhattan and are available at dispatcher lines at airports, but are harder to find in the other four boroughs. Some cabs accept credit cards for payment and all will be required to do so by the end of 2008.
Info on fares, flat fares, group rides and rules are online at the NYC.gov website. http://www.nyc.gov/html/tlc/html/passenger/taxicab_rate.shtml
Livery or Black Car
Known as car services or livery cabs, these cars may only be called by phone, are flat rate rather than metered (ask for the fare before getting in), and are not allowed to cruise the street or airports for fares. Their license plates will say either "Livery" or "TLC" on the bottom. Since yellow cabs are hard to come in the outer boroughs, limos are particularly useful for getting to the airport (your hotel can arrange one or look up the yellow pages). In some areas, livery cabs can be flagged on the street. Though this is technically illegal (the cabbie, not you, can get into trouble), it is useful in upper Manhattan and the outer boroughs and is accepted practice. Negotiate the fare before you get inside. A tip of 10-20% is expected and passengers must pay all tolls.
Tips of 10-20% are expected in both yellow cabs as well as livery cabs. A simple way of computing the tip is to add 10% of the fare and round up from there. Thus, if the meter reads $6.20, you pay $7 and if the meter reads $6.50, you pay $8. Always tip more for better service (for example, if the cabbie helps you with your bags or stroller). Don't tip at all if the service is lousy (for example, if the cabbie refuses to turn on the AC on a hot day). For livery cabs, tip 10-20% depending on the quality of the service but you don't need to tip at all if you hail the cab on the street and negotiate the fare in advance (leave an extra dollar or two anyway!).
All licensed taxis and sedan limousines are authorized to take 3 passengers in the backseat and 1 in the front seat for a total of 4. However, some of the newer minivan and SUV yellow cabs can seat more passengers and may take more than four passengers (even though the licensed limit is posted in the cab). Larger than sedan limousines can be reserved, also useful for airport trips with lots of luggage, by calling any of the dozens of companies in the yellow pages.
Be wary of unlicensed cars (known as 'gypsy cabs') cruising for passengers, especially near the airports. While drivers may claim to offer you a cheaper rate than an actual taxi, your chances of actually getting this rate (not to mention getting to your destination safely and quickly) are slim. If you are in doubt, ask an airport staffer for help finding a cab or cabstand. Major airports have taxi information cards for passengers.
For all cabs, you pay the tolls for bridges, tunnels and highways, even if the cab has an E-ZPass to use the express toll lane. Be careful of being overcharged by cabbies for toll crossings—on some bridges and tunnels (like the Queens-Midtown Tunnel) rates are not posted in plain view. So, a crossing which actually cost the cab driver $4 is easily passed onto the unsuspecting passenger as a $5 charge. Outside the city, other than flat fare destinations and Newark Airport, meter rates are doubled (when going to Westchester or Nassau County).
There are also bizarre van and shuttle services in different parts of the city. You will have to ask where it is going and how much it costs. Usually, you will see people lining up and some mysterious van will appear and they will board. There are services between Chinatown and Queens (you won’t have to make any transfers if it goes where you need to go!), and also there are separate services in Brooklyn, and Queens. Many of these services are branded as "Dollar Vans" (actually costing $1.25), and follow major bus routes. One should use good judgment before using these vans to prevent getting cheated out of money, or something considerably worse than losing money.