Ed Levine of NY Eats says quite a few of the best pies in the NY area are in Brooklyn. Check out this great list.

Corner (formerly Yura), Upper East Side
Two Little Red Hens, Upper East Side [note: what about Lady Bird Bakery? in Bklyn]
Clinton Street Baking Company, Lower East Side
Community Kitchen and Juice, Upper West Side
Sweet Melissa’s, Park Slope and Carroll Gardens, Brooklyn
Trois Pommes Patisserie, Park Slope, Brooklyn
Soutine, Upper West Side
Little Pie Company, Hell’s Kitchen and Grand Central Station,
Sarabeth’s, Upper West and East Sides and in Chelsea Market
Duane Park Patisserie, Tribeca
Wimp’s, Harlem
Mitchel London’s, Fairway, Upper West Side, and the Upper East Side
Bubby’s, Tribeca and Dumbo
Baked, Red Hook (I had a killer piece of apple pie there recently)
Briermere Farms, Riverhead, Long Island
Round Swamp Farm, East Hampton, Long Islan