Rogue Music is where musicians go to shed their post-tour gear. 251 W. 30th Street, 10th Floor, I believe, though that's from memory (it's in the legendary music building). While you're there, venture a block away to Scientific Plastics and be fitted for custom earmolds (get clear ones) and/or musician's earplugs. 15 streets away and two avenues down, on 14th Street, you can visit Guitar Center -- which isn't the best but is worth a purposeful loiter. Manny's and Sam Ash are worth a jaunt as well -- they're even on the same block.
Here's the tour as I might plan it:
Sam Ash/Manny's (48th Street off 8th Ave), Rogue (30th btwn 7th & 8th), Scientific Plastics, Guitar Center (14th Street) and, eventually, various Lambsie Divy used music stores in the East Village (such as East Village Music, at E. 4th St. off 2nd Ave, and Ludlow Guitars, at 164 Ludlow Street).
Call them all in advance and find out what they have. With Rogue, you never know.
If you can't find what you're looking for and need pedals (such as the Pod), an A/D converter and a mike pre as well as a guitar, then I suggest you try this site:
http://www.mercenary.com. It's not in New York, but you can barter with the Epicurean gent who fuels it. You won't find an Avalon 737 or Lucid A/D (or even a Great River) for less.