Rudy's in Ridgewood, Queens, is supposed to have amazing Linzer tarts -- I can't speak from experience but I have a Linzer tart-loving friend who swears they are among the best in the city.
----- Rudy's Pastry Shop 905 Seneca Ave, Queens, NY 11385
My favorite bakery is Leske's, 7612 5th Ave, Bay Ridge. I haven't tried their linzer tarts but their half chocolate dipped cookies are awesome. They also make some decent donuts in the morning.
----- Leske's Bakery 7612 5th Ave, Brooklyn, NY 11209