La Bergamote - their danish are BEAUTIFUL and yummy. They fruit danish seem to contain a custard of some sort?
Silver Moon - their milk bread.
Ceci-Cela - their petits fours (which you need to order in advance) are BEAUTIFUL and so delish for small house parties. They also have a breakfast pastry.. I think it's filled with like an orange cream.... that is awesome.
Goupil and DiCarlo - formerly in Chelsea Market, they seem to have disappeared? Anybody know where they went?!
City Bakery - their mini butter cookies and their mini choco cookies. And you have to try their pretzel croissants. Sounds weird I know, but they are addictive!
Sweet Melissa (Cobble Hill) - their choco peanut butter brownie is so delish, but very rich
TeaNY - OK, not a bakery per se, but their chocolate peanut butter bomb dessert is awesome. It litterally tastes JUST like a Drake's Funny Bone, but without the guilt of eating something by Drake's (mass-produced and probably filled with preservatives and artificial ingredients).