Prosecutors revealed Wednesday they have additional cellphone video from witnesses in Jordan Neely’s subway chokehold death, as ex-Marine Daniel Penny pleaded not guilty to manslaughter charges in the lightning-rod case.

The 24-year-old former infantry squad leader — who appeared in Manhattan Supreme Court clean-shaven and wearing a blue suit and maroon tie — was arraigned on charges of second-degree manslaughter and criminally negligent homicide during the brief, minutes-long hearing.

A stoic Penny spoke only to say “Not guilty” as more than 50 people — including his supporters, backers of Neely, 30,  and many members of the media — looked on.

The Long Island native was caught on bystander video putting Neely — who witnesses said had been threatening subway riders — into a chokehold on an F train on May 1. The medical examiner’s office later ruled Neely’s death a homicide.

Court documents filed Wednesday show that prosecutors have at least five cellphone videos from three witnesses to the deadly encounter that they plan to introduce as evidence.

They also have videotaped statements from two other witnesses, as well as two MTA surveillance videos and police body-worn camera footage, the document states.

Additionally, prosecutors disclosed they have a videotaped statement that Penny made to cops the day of the incident — when they released him without charges.

Penny’s statements to cops inside the Broadway-Lafayette Street station, as detailed in the filing, echo what he has said publicly about the incident since.

“He came on, threw all his s–t down, was very aggressive, going crazy. I was behind him, put him in a choke,” Penny said to the police at the time, according to the court document.

Penny described what could be seen in the shocking video of the confrontation, that Neely was “rolling, he was rolling, when he was in a choke. He was going crazy,” the filing states.

Penny also told police that Neely was “acting irate, dropping things on the floor, saying he doesn’t care if he goes to jail,” according to the court doc.

“He was pacing back and forth on the car,” Penny allegedly said. “I came from behind and put him in a chokehold. People in the subway were afraid for their safety.”

A freelance journalist who happened to be on the subway recorded the tail end of the fatal encounter, and the footage sparked immediate outrage after its release.

Penny surrendered to authorities on May 12 after the Manhattan District Attorney’s Office brought charges against him. He was indicted by a grand jury earlier this month and remains free on $100,000 bail.

He faces up to 19 years behind bars if convicted on both counts.

Penny has said he didn’t mean to kill Neely, but that he felt he had to step in for the safety of other passengers as Neely — who had a long history of mental illness — had been throwing trash at riders and threatening them as they moved away from him.

Thomas Kenniff, one of Penny’s attorneys, said outside court that the evidence in the case shows “our client acted reasonably under the circumstances and he was justified in the actions he took, however unfortunate the consequences.”

Penny’s other lawyer, Steven Raiser, said he believes their client will get a fair trial in Manhattan since New Yorkers are all too familiar with the dangers of riding city subways.

“They understand what it’s like to be on a subway, what it’s like to be confined underground, what it’s like to not be able to leave when faced with a threat,” Raiser said.

“So it is a very positive thing that we’re able to go to the people here in Manhattan and ask them to render a verdict on this case because they understand what it’s like to be in the situation that Daniel was in at least to the physical confinement.”

Raiser added that “this is a very trying time” for Penny.

“Daniel is a brave guy. He’s continuing with his schooling. He’s doing what he needs to be doing, staying close to his family,” he told reporters.

Neely’s family has called for heavier charges of murder to be brought against Penny and have claimed that the city’s mental health care system failed Neely — who also had a long history of brushes with the law.

Speaking outside court after the hearing, Neely family lawyer Donte Mills blasted Penny for not having “the courage to look Mr. Jordan’s father Andre in the eye.”

A legal defense fund set up for Penny by his attorneys had raised nearly $3 million as of Wednesday morning — with contributions from notable figures, including a $5,000 donation made by musician Kid Rock.

But Mills claimed that the legal defense fund couldn’t buy Penny a get-out-of-jail-free card.

“It’s not going to happen,” Mills said. “It didn’t work. You can ask for a refund. We are here.”

“Daniel Penny stands indicted for Manslaughter after allegedly putting Jordan Neely in a deadly chokehold for several minutes until and after he stopped moving,” Manhattan District Attorney Alvin Bragg said in a statement after the arraignment.

“I hope Mr. Neely’s loved ones are on the path towards healing as they continue to mourn this tragic loss.”

Penny is due back in court on Oct. 25.