South of 14th Street - for not too pricey, nice atmosphere and good quality food I'd recommend Cafe Cluny. Midtown west I've been a fan of 44 and X for a long time. It may be that I live reasonably close, but I've always enjoyed their brunch.
284 West 12th Street, New York, NY 10014
I tried Hundred Acres, Westville and Jane, they both serve pretty good brunch food.
I like the ambiance at Hundred Acres, and the food is not bad. Jane is also famous.. it's usually crowded on weekends.
But what I like best is Westville (18th street and 7 ave, I think). They serve homemade style brunch food, which I think is really good. They also have market vegetables, which changes everyday depends on what's in season. Last but not least, must try their coffee!! :)
38 MacDougal St., New York, NY 10012
246 W 18th St, New York, NY 10011
If you're willing to go slightly midtown-east, for a delicious but not too pricey brunch, I strongly recommend Artisanal. They're located on E. 32 St. between Madison & Park (the #6 train stops on the corner of 32 St. & Park for convenience). Artisanal has a fantastic French onion soup and beignets. They specialize in cheese (they also sell cheese right inside of the restaurant).