If you don't mind paying $15, Union Square Cafe is supposed to make a mean burger.
I love my turkey burgers from The Kitchenette (one is in Tribeca and another uptown) so i'm sure a regular burger is great too.
relish diner in williamsburg. their burgers are excellent.
Paul's on 2nd Ave (below St. Marks). I can't usually handle such huge portions of meat anymore, but they do alright. Beef & turkey burgers.
the Coffee Shop on the northwest corner of union square. damn good burger.