The numbers above are an exaggeration. I lived in the north end of manhattan (the part furthest from JFK) and an hour to get to JFK was on the long side - typical is probably 40-80 minutes. It doesn't take two hours to clear security at an airport either - typical is anywhere from 10 to 45 minutes.
The problem is you have to allow extra time in case something has gone wrong. I waited two hours in a queue at O'Hare just to get through security - thankfully I had allowed three hours.
Compare that to anywhere in Australia where you can be sure security won't take more than 10 minutes - you can arrive at the airport with 45 minutes before your flight and still be waiting 20 minutes after you check in and pass security before you board.
Incidentally, Uber direct to JFK is slightly cheaper than a cab too ($45-ish?). You think it would be crazy expensive, but it's flat rate. I'm not sure about from JFK into the city, but I think I was told it was the same.
I'm not too big of a fan of the AirTram + Long Island Railway (LIRR) route, which ends up at one of the major train stations, has on outside terminal (not great in the winter and slow with a lot of things to remember to do), but is about half price of that.
I've become a big fan of the AirTrain + LIRR combo since moving into Manhattan from Brooklyn. Almost always consistently 45-50 minutes from terminal to my apartment in Chelsea. Perfect for rush hour to/from JFK.
Uber to JFK is $66 right now. Taxis are a flat rate to JFK as well ($60 plus tip). There are car services you can call which will do it cheaper.
I've recently started doing Penn Station -> Jamaica w/ LIRR -> AirTrain, it's miles better than subway and almost preferable to car if you're paying for the car.
Uber flat price to the city is great until you hit a surge, which is easy to hit in the afternoons, especially when it rains. Then it can be 2x or 3x the price of pre-booking a ride. Uber should add reserve pricing for trips you know in advance, like AWS does.
