I don't know that I could answer that question with much authority. A while back, there was a huge burger list on RF of NYC places and I've only been to a few of them. This is a list that Pigiron made:
Back 40
Better Burger NYC
BLT Burger
Blue 9
brgr
Burger Joint
burgers and cupcakes
Five Guys
goodburger
Kool Bloo
New York Burger Company
Pop Burger
Rare
Sassy's Sliders
Shake Shack
Stand
The Twisted Burger
Zen Burger
Zip Burger
Ziggaz
And there are probably 10-20 more in the city as of today. So far I've been to:
1.) Blue 9 Burger-Good burger of the thin variety. They use the burger diaper mostly seen in Southern California and no need for ketchup on this one. They have a special sauce that pairs nicely with the meat. Haven't been in about a year and half, so not sure how it stands up today.
2.) burgers and cupcakes-Excellent burger, thick, juicy. Bun is top notch too.
3.) Five Guys-Love this burger! Always cooked medium well, yet always very moist with a great crust and lots of flavor.
4.) goodburger-Not at all impressed with this one. Not bad, but I didn't think it was anything worth a special trip.
5.) Shake Shack-Good, solid burger, but not the best I have ever had. Must be okay with waiting in fairly long line for this one.
6.) Burger Shoppe-
7.) Carneigie John's street cart- NYCFoodGuy put me on to this $4 cheeseburger at a cart located outside of Carneigie Hall. Moist, messy and nice balance of char from the grill and crust from the griddle.
8.) Jeremy's Ale House-I wasn't mad about this burger. It tasted like the pre-formed from the box variety.
9.) Zaitzeff-Very moist and juicy, always cooked perfectly, but can be a bit pricey for what it is. I realize this isn't the best pic, but it's the best one I had.
10.) COMIX-My girlfriend and I had a really juicy, thick burger here while seeing some comedy and I was surprised that such a good burger could be found in a club. The bacon & cheese on it were top notch too.
11.) Island Burgers & Shakes-Very thick, not very juicy (but in hindsight, I should have ordered it medium rare). Toppings and bread choices are key here too.
If I had to pick my favorite of these, I'd go with Five Guys. I just love it and find it on my brain whenever I crave a burger. If I were to pick a place that is only in NYC, I would go with burger and cupcakes and Carnegie John coming in a close second. TTM has been saying I've gotta get to the Burger Joint, so I think that'll be my next stop.