High-end ukuleles in NYC are a rare commodity. I'm in Manhattan 1-2 times a week and the only place I can recommend for any kind of selection is Matt Umanov's. Had a few Martin's, Kamakas, and some vintage (Gibson, Martin, Kumalae and Kamaka) stuff. Even then, pretty slim selection.
I have not been to Mandolin Brothers on Staten Island, but based on their website they have a few Kamakas, a Collings, Martin, and Flukes.
And yes, East Village Music has odd hours. Make sure you call even if you go during when they say they're open. And ask about what they have... the website isn't always up-to-date. I've purchased a couple of ukes from them without problem before, but won't bother checking anymore because a couple of trips I've called and then made the trip to the store only to find the doors locked. I was hoping to check out the used Kamaka Soprano Deluxe they had on the website.
If you're a guitar player too, for fun check out Rudy's Music in Soho. Beautiful store. They had a number of Flukes in the acoustic room last week. At least you quell your 4-string jones.