Rudy's on 48th
Sam Ash across the street also on 48th (used to be Manny's)
Guitar Center on 14th in Union Square
30th Street Guitars...on 30th

Ludlow Guitars on Ludlow
Matt Umanov on Bleeker
Mandolin Brothers on Staten Island
You can call and schedule an appointment at Aguilar, they're on the corner of Broadway & Houston. They got some nice stuff to play as well.
I know Rudy's has some Bergs, but mainly just the small stuff. I got a nice attitude from the salesman when I asked if they happen to have anything larger, an NV610, like I was a idiot for asking such a moronic question in NYC.
I'm not sure that anyone has Genz or EBS in the city, the well traveled stores at least.