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:
Better Burger NYC
burgers and cupcakes
New York Burger Company
The Twisted Burger
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.