JFK is at the end of a long subway line, with the Air Train between the subway and the airport. Coming from most parts of Manhattan, I would budget 90 minutes to get there via the subway and 45 minutes by taxi.
The subway to JFK is cheaper, but most people who live in Manhattan and can afford to fly semi-regularly are going to spring for a taxi.
The subway to JFK is cheaper, but most people who live in Manhattan and can afford to fly semi-regularly are going to spring for a taxi.