AT&T has admitted that their cell network is having difficulty coping with the surge in data usage by smartphones -- much of which the iPhone is responsible for. Dense areas like NYC would be hit hardest by demand, so it's possible AT&T was trying to prevent its network from collapsing in the region.
If that were the case though, you'd expect sales to stop elsewhere, but the iPhone was still available through AT&T and Apple retail outlets. It has also been suggested that the carrier was attempting to reduce fraud -- though, that also seems unlikely.
Regardless of AT&T's logic, might this be a sign that Apple should finally extend the iPhone to other providers?