I'm trying to put a list of places together on where to go to get great desserts, not just at the top restaurants in the city. The kinds of places you don't necessarily have to eat a meal at either...
You may want to check out Room 4 Dessert, Will Goldfarb's fairly trendy new place. Everything is prepared by he and his staff at a bar, so it's a cool visual. The desserts are unusual though (frozen things, foams, odd but neat flavors), so perhaps not for everyone's taste.
And I agree with the posts above - The Tavern Room @ Grammercy is always a hit - more traditional desserts, nice dessert wine / liquor list.
Café Mozart (W70th & Broadway). They have an awesome dessert menu that will satisfy any and all cravings. I was there recently with several girlfriends for dessert fest. We ordered the chocolate fondue for the table and then we each made selections from the extensive desert menu. Every three bites we passed the plates to the left.
The Little Pie Company is a real NY story; it was started by a struggling actor who baked pies in his apartment to subsidize his income. He has since given up show biz and operates 3 shops in the city. The original shop is located at 43rd street (btw 9th & 10th Aves); there is one on W14th St. (btw 9th & 10th Aves.) and there is an outlet in Grand
Central Terminal. My favoriate item is the Sour Cream Apple Walnut Pie
Finally, I have to give a shout out for The Chocolate Room located in my backyard; Brooklyn (86 Fifth Avenue, between St. Mark's and Warren) This place is a charming intimate desert café that will have you floating on cocoa bean high.
This may be like interrupting a discussion of the relative merits of Ferran Adria and Thomas Keller with a story about a nearby hot dog stand, or telling a guy waxing eloquent about Babe Ruth what a great little leaguer your son is, but... Egg Custard King Cafe in Chinatown is worth a try. They are wonderful. Someone posted about this place several months ago and whenever I'm in Chinatown, which is often, I cruise by. The problem is, they are usually out of custard tarts (I go late evening) Twice I've snagged them. There's usually a crowd of elderly Chinese ladies around the counter when the tarts came out. I imagine them telling their sons, I slaved all day to bake this for you because nothing is too good for my boy! And if you like that kind of place there are Uruguayan bakeries in Queens and Portuguese bakeries in Newark where you can find the nata, the original version of what Custard King calls "Portuguese" tarts.