Gov. Cuomo bounced one of his newest MTA-board appointees last week — a move that came because his pick was too “independent,” sources said.

Michael Lynton, 59, former chair of Sony Entertainment and current board chair of the company that owns Snapchat, was booted after only two months.

His removal came because he was unwilling to kowtow to Cuomo, according to someone who knows the businessman.

Lynton declined to comment.

A Harvard MBA, he has served on numerous corporate and nonprofit boards, including at Warner Music, Pandora, Lincoln Center, the Smithsonian and Harvard.

“It was a big surprise that he would join the MTA board in the first place, because he’s an actual grown-up with major real-life experience,” said John Kaehny, head of Reinvent Albany, a watchdog group.

Kaehny said Lynton had the most management experience of any on the board.

“You’d have to think he was completely competent,” Kaehny said. “Therefore, it would have to come down to a question of independence and whether he was doing exactly what the governor scripted.”

Cuomo denied that in an interview with The Post.

He said he was merely “substituting players” to deal with the crisis at the Long Island Rail Road, where overtime costs are soaring amid the lack of a modern timekeeping system and the alleged sabotage of a digital time clock.

Last week, a cable was found cut on a fingerprint scanner due to be installed at the LIRR Jamaica station in Queens. And on Saturday, another time clock was found apparently vandalized at the MTA’s 38th Street train yard in Brooklyn.

Cuomo also pushed out Fernando Ferrer, the MTA board’s vice chair whom he appointed in 2011.

“We need the talent to respond to the crisis,” he said. “It’s not a reflection on Freddy. It’s not a reflection on Lynton. They’re both extraordinary guys.”

Cuomo’s proposed replacements are close allies — state Budget Director Robert Mujica and Linda Lacewell, the governor’s former chief of staff who now heads the state Department of Financial Services.

Mujica, of Albany, does not meet the residency requirements for board members, but Cuomo said he would ask the Legislature to change the rule for Mujica.

A Cuomo spokeswoman said the governor’s office was working to appoint Lynton to another state board.