Surprisingly I have never flow thru JFK, but a lot thru Newark and a few times via La Guardia. What I remember most is that I flew into Newark (a big hassle) and few out of LGA as my first experience with that airport. I enjoyed LGA as they have signs to the rental car return.
Before Newark consolidated their rental car area, if you missed the turn the only way you could find a rental agency was to find and follow their Bus. I hate/hated flying in/out of Newark (and I almost never use the word “hate”)
I have experienced all three airports, leaving from Manhattan, NJ or Westchester county.
The train to Newark airport from Manhattan is cheaper and faster than anything from Manhattan to JFK or LaGuardia. For $13, after leaving Penn Station New York, it takes 25 minutes to the 3rd stop at an end-stop of the monorail that goes around Newark airport. The monorail delivers you to the inside of each terminal, just an escalator ride down to check-in, and/or the car rental building. Neither JFK nor LaGuardia have that kind of access, at any price (minus horrendous subway/bus trips).
From Westchester county my pick has usually been JFK even though La Guardia is closer (usually international flights)
From NJ, for domestic flights there is no contest - Newark, while for some international flights its often been JFK.
Before 9/11, Newark was easy for short-term parking to drop of or pick up someone. You could get very short term parking right under the terminal building with a very short walk to entrance that was one escalator ride away from the arrivals level or two from the check-in. Then came 9/11.