I am on a quest to find THE best huevos rancheros in the city. I have tried the ones at Five Points and the Smith. These were passable but there must be better.
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I've had great versions at both Cookshop (it's a relative of Five Points, but I don't know how similar the preparations are) and Clinton St. Baking Company (my favorite, but not based on a large sample).
Prune has a good version at brunch- but either go early or deal with the wait.
Cafe Habana is also pretty good.
Cookshop is usually great but sometimes not- really inconsistant.
Salvation taco has chilequiles that are not the same but worth mentioning
I don't know if it's the best as I don't alway order it, but Clinton Street Baking's version was always enjoyable.