The best kept secret in NYC is:
Shopsin's
Of course many NYers know about it, but I am surprised how many do not. The family that runs it is very eccentric. The food is amazing b/c not only is it quite good, but it's very hard not to find something to eat that you have never even dreamed of. My breakfast of a Bacon, Egg and Cheeseburger with Egg & Cheese French Fries was superlative! (Im at Shopsins about 2x a week now).
The menu must be seen to be believed...even more amazing is how they make everything taste so good with such a wide range of ingredients. I think their small place and strict rules limiting parties to 4 is what makes that work.
http://www.shopsins.com/media/redshops/shopsiemenu.pdf