Another vote for Bruckner Hobbies, a bit out of the way from Manhattan, and hard to get to without a car, but the best I've found in NYC, especially for Tamiya bits.
Sorry to say, but I spend most of my time between the Tower Hobbies and Tamiya USA websites.
If I may add, you can always check out the Chelsea Flea. http://travel.yahoo.com/p-travelguide-2736...new_york_city-i
I came back with an original Wild Willy LWB, almost complete and never run, for $65.00 recently.
Best of luck.