Two kayakers were found dead in the waters near Hampton Bays, Long Island early Wednesday — a day after they were reported missing, cops said.

The bodies of Daniel Villa, 25, of Southampton and Juan Carlos Penaranda, 43, of Quogue, were recovered from Shinnecock Bay.

Police say the men embarked from Ponquogue Pier around 8 p.m. Tuesday, using a singular two-person kayak to head west through Shinnecock Bay.

Daniel Villa, 25, of Southampton, and Juan Carlos Penaranda, 43, of Quogue, were found dead in the waters near Hampton Bays, Long Island, early Wednesday. Edmund J Coppa

Family members of the deceased reported them missing around 1:30 a.m.…