Rental Car major companies have stations in each terminal at the airports, these are located in arrivals, they also offer free shuttle service to places to pick up the car.
Hertz JFK: Building 318 Federal Circle New York City (Jamaica), New York 11430-9508 United States Phone: 718-656-7600
Schedule: Monday - Sunday/ 24 hours
Hertz New York City La Guardia Airport Marine Air Terminal Building 22 New York City (Flushing), New York 11371-1041 Phone: 718-478-5300
Schedule: Mo-Su 24 Hours
Hertz Newark Building 318 Federal Circle New York City (Jamaica), New York 11430-9508 Estados Unidos Phone : 718-656-7600
Schedule: Mon-Sun/ 24 Hours.
Try renting the vehicle online, before arriving at the airport, this way you could have a discount on rental prices, be sure to use a credit card and no debit to avoid any inconvenience when you are giving back the car.