A Long Island man killed in a boating accident over the weekend has been identified, while a second man was still missing, cops said Sunday.

Farmingdale resident John Costa, 54, was trying to navigate his 22-foot angler in “rough water” near Jones Beach inlet when a series of large waves caused the vessel to overturn, Nassau County police said. He and three passengers ended up in the water.

Good Samaritans on the boat named the Brett Allie 5 recovered two people, a 24-year-old and 26-year-old man, that were clinging to the vessel’s hull and wearing lifejackets, officials said. They were transferred to South Nassau Medical Center with minor injuries.

Costa was recovered and pronounced dead at a hospital, officials said.

Eleven boat crews and four helicopter crews conducted a search — including three boats and two helicopters from the Coast Guard — which covered a combined 655 square miles searching for the fourth passenger, Coast Guard Station Jones Beach said in a news release.

“Our deepest condolences go out to the families and friends of those who were lost and affected by this tragic incident,” said Cmdr. Valerie Boyd, a search and rescue mission coordinator with Sector Long Island Sound.