I know seriouseats has written about kyotofu before, but their baked goods are seriously divine. and the right portion size too. I just had one of their awesome hazelnut chocolate chip cookies and a mini chocolate chip cupcake that doesn't need any icing but is pure, perfect cake.
I was reading a thread about hidden gems in nyc neighborhoods before and I think kyotofu belongs on the list for hell's kitchen/clinton.
other places I love: petrossian for croissants, taboon for brunch (I like their eggs with merguez). Any other suggestions from people who live/work in the neighborhood?