Have you considered picking up the car in NYC and doing a one-way rental to JFK? It may be easier/less expensive. I live in NYC and that would be the first thing I would check.
If there is no difference in price and between JFK and LGA, you would want to pick up from LGA as it is much closer to the city than JFK. One thing to note is that LGA airport is a bit of a mess these days due to construction, but even accounting for that, it's still going to be faster/more convenient to pick up at LGA. If you take an Uber there (my recommendation), be sure to put in the Hertz office address since it's not near the main terminal area, and if you go into the airport proper and follow the signs, you're just going to waste a lot of time.
Hope this helps!
Last edited by AutoSlash; Apr 28, 2017 at 5:24 am