I'll add The Breslin (John Dory also supposed to be solid, but never been), and No. 7 sub for some weird and delicious sandwiches.
ABC Kitchen, although that might be a bit too south and east for what you're looking for. Ciano is in Flatiron--haven't been yet but gets a lot of love on this board. I'll attest to Aldea being very good. City Bakery if you're into the absurdly-rich-hot-chocolate thing (never tried their food).
Coffee-I enjoy Stumptown, Birch
Beecher's for happy hour, Boqueria for dinner, Eataly for vittles, Hill Country Chicken for hill country chicken, Shake Shack, Boqueria, Bottino to go for sandwiches, Bar Stuzzichini for dinner. My husband likes Resto a lot but I've never been. And Aldea is supposed to be great!