Yes, NYS handgun laws are a joke. Arbitrary, ridiculous, inconsistent. Probably a violation of the constitution, even with the most narrow reading of the second amendment. (An obvious violation under Heller, in my opinion.)
On the other hand, as a practical matter, ever been in midtown Manhattan? I defy you to find a safe direction to point a gun. Seriously. So I can understand the temptation to ban them under that circumstance. It's pointless and stupid, because people will do the stupid thing anyway.
It infuriates me that NYC's problems become the problem of the whole state, and that they would like to make it the problem of the whole country. I'm glad to hear that you got your permit. The excuse the clerk gave you when you applied sounds like typical bureaucratic BS, someone trying to head off a complaint before it happens. Not even NYS is that incompetent.