The Ear Bar has been in New York longer than any of us. In a city of vacuous fleeting trendy bars the Ear Bar (which is really called the Ear Inn but I've never called it that) is the real deal.
Mekelburg's is equal parts hipster bodega, bar and sandwich haven. I always go for the cheese counter, the babka and the late night fried chicken sandwich, which is hands down one of the best I've had in NY.
The reputation of Mission Chinese Food is for being cool, weird, and extremely eccentric, which tends to mean that you either love it or hate it (an assessment that is at least somewhat correlated to your personal tolerance for spice).
My favorite Japanese restaurant in NY...Small and cozy place, the staff is great, the food always simple and delicious, the uni shots are addictive and the sake perfect.