Zarela's on 2d Avenue in the 50s, has outstanding chiliquiles. A bit different from other spots. Tortilla chips, shredded chicken, much tomatillo sauce and lots of chihuaha cheese. All baked till molten and starting to brown on top. Served in a large porcelain dish. I've had a lot of chiliquiles but those are the best I've had in NYC.
Tulcingo del Valle, they make green and red, and also have a "with steak" option that you should pass on, unless you just happen to want a decent piece of meat. They always say the red is spicier, but the green is. I like the green cuz it's tangier.
(if you don't already know, chilaquiles is "mexican lasagna made with corn tortillas instead of pasta and spicy salsa instead of red sauce", mexi-cheese on top)
At Tulcingo, they come with excellent refried beans. BTW, the food is widely acclaimed to be truly authentic, but I will point out that this dish is vegetarian friendly and therefore is not made with lard. Has cheese though, so not vegan.
If this is "a trip" for you, while in the neighborhood be sure to walk a half block up and try the tacos in the back of the quirky bodega called Tehuitzingo. Be sure to get the potato, with and without meat, both are sooooo good; without meat is also vegetarian friendly. (acutally, I'd go to Tehuitzingo first, grab just a couple of tacos, then walk down to Tulcingo, is how I would do it.
Tulcingo del Valle
665 10th Ave, New York, NY 10036