Are you looking for all-boys? I don't know of any all boys publics (maybe a couple of random charters in bad nabes).
Private SS - Collegiate, Browning, Xavier, Fordham Prep (Bronx). For co-ed private, Poly Prep in Brooklyn and the Hill schools (Riverdale, Fieldston) are probably the best.
Public - all the large selective HS have great sports (Stuy, Bronx Sci, BTech), and Beacon, Eleanor Roosevelt, and Clinton (all Manhattan) come to mind.