You’re right, the taxis in NYC (the yellow ones) charge a $45 flat fee from JFK to Times Square, which includes a toll if the taxi is taking the Queens-Midtown Tunnel, one of the major East River crossings into the city.

The airport express motorcoach charges about $15 from airport to either the Port Authority Bus Terminal or Grand Central Terminal. Public transit is the cheapest way to go if you want to save some cash.

Now, there are two ways to get from JFK to Times Square.

Option 1, you can take the subway (underground) straight to the Port Authority Bus Terminal, which take about 45 to 50 minutes. Once you exit the subway at the PA Bus Terminal, you can walk a block east to Times Square.

or

Option 2, you can take the Long Island Railroad, which is a commuter railroad, from Jamiaca Station to Penn Station and then the subway from there to Times Square. The trip by commuter rail will take about 25 minutes, with about a 2 minute ride on the subway from Penn Station to Times Square.

The link below has all the information you need to know about getting from airport to Times Square, including fare information on both the subway and the commuter rail, as well as fare information on the JFK Airtrain, which is an airport peoplemover that connect the airport with Jamaica Station.

I hope this information is very helpful. If you have any questions or need travel directions while in town, just drop me a line by clicking on the avatar and e-mail icon in the profile. I’ll be glad to help.

Good luck
Native New Yorker

the NY Airport service bus is now only $7 from JFK to Manhattan.
http://www.nyairportservice.com/

or the shuttle for $17
http://goairlinkshuttle.com/