I've just returned from New York and arrived into JFK. The fixed fare is $45 plus toll (tunnel/bridge) plus. All in all cost us about $55-60.
If you are handed a piece of paper by the cab officer (there is a marshall organising the queue) it does say on there that the flat fare of $45 plus extras applies on the return journey too. Drivers don't seem to be aware of this, we had one who was reluctant to do it until we showed him the paper, he then said that it would work in his favour anyway.
I think it depends on the time of day you return, rush hour on a meter would cost a lot more than $45!!
Arriving in New York and then navigating the subway system I think would be difficult (esp. if it your first time). The stairs at stations and then finding your way form station to hotel can be stressful if you don't know where you are going.
Some subway trains are classed as Express and don't stop at all stations (you could be sat on the train and watch your destination pass you by!!).