Depends where you go in the New York area.
The average tourist will not look much further than Manhattan / Times Square area, or the airport area if overnighting.
I personally have no issues staying in Queens etc. and hotels here are quite often far, far cheaper than in Manhattan.
It's a case of having a little knowledge of the area or to be willing to step out of your comfort zone area wise when it comes to booking something.
As mentioned earlier, the Jersey Courtyard was picked up a couple of days before the marathon. (To be honest, it still takes about 3hrs or a good marathon day to get from Queensboro' Plaza etc. to Staten Island using the subway to South Station then the ferry and bus).
It's possibly a little bit far out for JFK and/or marathon purposes, at least for runners (spectators may pop along later and be more local so can drive to the hotel and then use public transport at their discretion).
Some places in Brooklyn aren't that close to subway lines and are perhaps not in areas you would want to be wandering about in at 5am or whatever.
$55 or whatever for a cab to the city on top of a hotel that probably costs £200+ is a chunk of someone's budget, especially, when mentioned previously, that Disney / SeaWorld are pretty much places where you might as well hand over your credit card at the gate and say "go nuts!"