Back in the day, reputed Bonanno crime family captain Nicholas “Nicky Cigars” Santora was a man to be reckoned with. As head of a crew working out of Brooklyn and Queens, he rose to the rank of family underboss.

But today, the 74 year-old Santora is lying in a Nassau County hospital bed, suffering from head injuries and barely conscious, allegedly because of negligent and malicious treatment by the New York City Department of Correction, according to a lawsuit filed earlier this week in Manhattan state court.

Since 2013, Santora has remained held without bail in a city jail after the Manhattan District Attorney’s Office indicted him and other reputed mobsters and associates for enterprise corruption. After a lengthy May trial, a Manhattan jury failed to reach a verdict and a judge declared a mistrial. Prosecutors want to retry the case.

Over the year’s Santora has suffered from vertigo and it was during his incarceration that the problem became more serious, leading to falls in jail and even falls out of his wheelchair, said his daughter Gina Santora, with whom he had lived in Franklin Square before his recent hospitalization.

“By time he went to Rikers, my father fell over a dozen times,” Gina Santora, 45, said during a telephone interview. “My father has sustained multiple head injuries . . . I watched him deteriorate literally.”

“It is baffling how many times he fell before they realized ‘Hey this guy needs a wheelchair,’” she later said in an email.

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Rego Park attorney Michael E. Talassazan, who filed the lawsuit on Nicholas Santora’s behalf, said his client was finally granted bail after the mistrial in May 2016 but since has been mostly unconscious and unable to communicate. Gina Santora asked that the name of the hospital be kept confidential to protect her father’s privacy and also that her married name not be used for this story.

According to the complaint, numerous bail applications had been made earlier in the case but were denied despite strong evidence that Santora was not involved in the crimes alleged in the case. The complaint also accused the Manhattan District Attorney’s Office of using a telephone call between Santora and his son-in-law to “fabricate a tale” that he attempted to smuggle a weapon into the jail.

The lawsuit alleges that correction officials failed to give Santora proper medical help and care, all in violation of his federal constitutional rights. The suit brings claims for medical negligence, intentional harm and violation of correction laws, as well as other assertions. The claim makes no mention of a specific dollar amount sought.

A spokesman for the city Department of Law would only say the lawsuit was under review.

Santora is a man with a significant criminal record and has had stints in federal prison. In 2012, he was sentenced to 20 months on a federal charge of extortionate extension of credit.

While deemed by law enforcement as an important member in the Bonanno family, Santora apparently had constant money problems and was once called a “brokester” by former family boss Joseph Massino. Gina Santora said she is pressing the lawsuit as a personal mission.

“I will be voice for any and every daughter who had to watch their father treated inhumanly by the New York City correctional system,” she said.

Meanwhile, Santora spends her days at her father’s hospital bedside, holding his hand and telling him she loves him. “Every few days he opens his eyes and tells me that he loves me,” she added.