A sister of the Boston Marathon bombers was busted in New York City Wednesday for allegedly threatening to blow up her live-in lover’s baby mama, The Post has learned.

Ailina Tsarnaeva, who lives in North Bergen, NJ, allegedly phoned the woman at her Harlem home on Monday and warned her to keep her distance or face explosive consequences.

“Leave us alone. I know people who can put a bomb on you,” Tsarnaeva, 23, allegedly said.

Law-enforcement sources said Tsarnaeva’s boyfriend, George Briones, is currently embroiled in a bitter custody dispute with his ex over their three kids.

The woman told cops about Tsarnaeva’s alleged call, and Tsarnaeva turned herself in at Harlem’s 30th Precinct station house, where she was charged with aggravated harassment and later released, sources said.

No one answered at the alleged victim’s apartment Wed­nesday evening, and her mom refused to comment when reached by phone.

But a neighbor in the building said the woman had obvious problems with her love life.

“I heard her talking with a friend in the lobby, [saying] that you cannot trust men, they are nothing but trouble,” the neighbor said.

Tsarnaeva’s arrest marks at least her second brush with the law, following a 2011 charge tied to a counterfeiting case in Boston.

Prosecutors alleged that she knew the customers who left a fake bill to pay their tab at an Applebee’s restaurant in Dorchester, and that she lied to a detective who questioned her.

Tsarnaeva skipped bail after getting busted on an obstruction charge. The case against her was later dismissed, according to a published report.

Tsarnaeva’s brothers, Tamerlan and Dzhokhar Tsarnaev, planted the homemade bombs that killed three people and injured more than 260 others near the finish line of the Boston Marathon on April 15, 2012, the feds have charged.

The brothers are also suspected of gunning down MIT cop Sean Collier three days later, shortly after the FBI released surveillance photos of them at the marathon.

Tamerlan, 26, was killed in a shootout with cops but Dzhokhar, 21, escaped, prompting a daylong lockdown across Boston. He After the lockdown was lifted, Dzhokar was found wounded and hiding in a boat stored in a Watertown back yard.

He was captured without incident and is awaiting trial.

On Saturday, Tamerlan’s widow, Katherine Russell, was photographed holding a baby outside the home Ailiana also shares with sister Bella, who was busted on pot charges following a domestic incident last year.

The following day, Ailina told The Post that Russell — who converted from Catholicism to Islam — had recently re-married and that the baby was hers.

Additional reporting by C.J. Sullivan and Frank Rosario