When you say "NYC" do you mean at an airport or a local edition? If the latter, as noted above, the discrepancy in my case was at a local edition in NYC (i.e. in the city). I just returned the car yesterday and was charged $490, which is what I was quoted at pick-up (i.e., not what I was quoted by priceline ($477) or hertz.com ($503)). And all three of these had the same base rental fee (~$407).

I am also told every time I use points that I will get charged the taxes/fees, but when I actually rent, I pay $0 (again, at local edition in NYC).