This kind of question is so difficult to answer, mainly because there are some places that have absolutely phenomenal homey food, but it's not anywhere near the level and class of upper-end places.

That said, if I have to pick one place that is absolutely at the top of my list, it goes to Chef's Table at Brooklyn Fare. Incredibly innovative food, with every course (of which you get 15-20, so keep in mind these are more bites / small portions) being absolutely phenomenal. I would love to go back again sometime, but there is so much good food in NYC (and getting a reservation is nearly impossible) that I probably won't be going back anytime soon.