Never been to NY, but everybody I know who has and is into fishing raves about the Urban Angler
You could shop online at Bass Pro, Cabelas etc. and have them delivered to where you are staying, but it's always useful to be able to try waders and boots on beforehand.
Check out waders and wading boots from Simms or Patagonia - these are the two best brands out there.
If they are too expensive, look at Orvis when you are over there.