NEW YORK — With the outcome already decided in the waning seconds, St. John’s students couldn’t resist.

“Who’s your daddy? Who’s your daddy?” came the chant in a crowd of 12,310 at Madison Square Garden.

Father was best in this family affair.

Rick Pitino defeated his son again Sunday in their latest coaching clash, as No. 22 St. John’s (4-0) passed its first real test this season by topping New Mexico 85-71 behind 21 points and 11 rebounds from RJ Luis Jr.

Richard Pitino, coach of the Lobos (3-1), didn’t seem to mind the catcalls too much.

A huge New York Yankees fan, he immediately recalled the origin of that derisive chorus, directed by Bronx Bombers backers years ago at Boston Red Sox pitcher Pedro Martínez.

“Other than that, I laughed it off. I didn’t think much of it,” said Richard Pitino, who attended a World Series game at Yankee Stadium with his dad last month. “This is what our obnoxious New York fans do, and I’m part of it.”

Rick Pitino wasn’t thrilled, though.

“I don’t get upset at the crowd,” he said. “I just wish they would stop saying that.”

Rick Pitino, in his second season at St. John’s, improved to 3-1 in coaching matchups against his son. The previous two wins came when the 72-year-old Hall of Famer was at Louisville.

Richard Pitino beat his father’s Iona team two years ago at The Pit. That’s one of only two victories by sons in 22 coaching matchups vs. their dads in Division I history.

“OK, he’s my son so I’m going to brag on him: He is a great young coach. Great young coach. His offensive mind is brilliant. He puts you in situations that really hurt you defensively,” Rick Pitino said.

“He’s got a great team this year. He does it with all new players, different players. He’s one of the bright young offensive minds in the game today. So, he’s a lot different than me. He handles losing much better than me.”

Other separators are easier to see.

Always a sharp dresser, Rick Pitino paced the sideline Sunday in a charcoal gray suit and snappy red tie. A few feet away, Richard wore a long-sleeve New Mexico mini-zip with track pants and sneakers.

Right after the final horn, they met for a quick embrace and headed to the handshake line following New Mexico’s first game at Madison Square Garden since the 1990 National Invitation Tournament.

“So much fun to be a part of,” said 42-year-old Richard Pitino, an assistant coach under his father at Louisville. “Although we didn’t win, I’m very, very grateful that my dad agreed to do it, and I’m grateful that my players were able to experience something like this.”

But he doesn’t expect pops to bring St. John’s out to Albuquerque to play at The Pit anytime soon.

“He would never do it, but I would love for him to do it,” Richard Pitino said.

“If I go back to Iona in a few years, I’ll go back to The Pit,” Rick Pitino said, drawing chuckles.

Rick Pitino said his daughter, Jacqueline, and another son, Ryan, would sit behind the St. John’s bench and stay neutral. But his wife, Joanne, made no secret about her plans to sit behind the New Mexico bench with her sister and best friend and root hard for Richard.

“‘You’re my blood. He’s not,’” Rick Pitino recounted his wife telling Richard. “So, it shows you how much she loves me and how much she loves Richard.”

Nelly Junior Joseph, who played for Rick Pitino at Iona before transferring to New Mexico, had 16 points in the loss.

The game marked the NYC Hoops for Heroes Classic benefiting the Tunnel to Towers Foundation, a very meaningful organization to the Pitino family. Rick Pitino’s brother-in-law and closest friend, Billy Minardi, was killed in the 9/11 attacks on the World Trade Center.

“I think the way The Garden got behind the game, I thought it was unbelievable for me, and my son will remember this forever,” Rick Pitino said.