Penny, 24, surrendered earlier in the day at the NYPD's 5th precinct where he was placed under arrest and handcuffed.
He appeared in court in the same white shirt and grey jacket, handcuffed as he entered under police guard.
Penny surrenders and his lawyer speaks to reporters
"The backdrop of this May 1 incident is presumably somewhat known," assistant district attorney Joshua Steinglass said.
He said prosecutors conducted a "thorough investigation" that included interviews with eyewitnesses, 911 callers and responding police officers before moving forward with the criminal charge that carries a maximum of 15 years in prison.
As Penny awaited arraignment, attorneys for Neely's family held a news conference, saying the family disagrees with the decision to charge Penny with manslaughter.
"We knew that justice would not be swift. We realized that justice was going to be a journey," said attorney Lennon Edwards. "Today we are not going to stop until we have full justice. We are going to pause to recognize that we have taken the first step, a step in the right direction."
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Edwards and attorney Donte Mills argue that Penny's decision to use a chokehold rather than a less lethal form of restraint, such as a bear hug, indicated that he intended to kill Neely.
He should therefore be charged with first degree murder, they said.
New Yorkers react to charges against Daniel Penny
Jordan Neely entered the northbound F train at 2nd Ave station and several witnesses observed him making threats, Steinglass told the judge during Penny's arraignment.
Penny held Neely for several minutes. At some point Neely stopped moving.
Penny continued to hold him for a period of time and then released him, Steinglass said, noting that Penny remained on the scene to talk with police.
Prosecutors sought Penny's release on a $100,000 cash bond, the surrender of his passports and a prohibition on travel outside of New York without the judge's permission.
Defense attorney Thomas Kenniff said Penny lives in New York City and attends college, pursuing a bachelor's degree in architecture.
"I have absolutely no doubt that Mr. Penny would return to court if your honor was to set no bail conditions, we are certainly amenable and join the People in asking for the bail package that was outlined by Mr. Steinglass," Kenniff said.
"My client has been fully cooperative throughout this process."
Penny enlisted in the US Marine Corps and served four years before being honorably discharged.
"There is nothing less indicative of flight risk than someone voluntarily surrendering," Kenniff said.
The judge approved the bond, clearing the way for Penny's release. The next court date is set for July 17.
The case will still be presented to a grand jury in the coming days as prosecutors work to secure an indictment, Steinglass said.
Manhattan District Attorney Alvin Bragg released the following statement:
"After an evaluation of the available facts and evidence, the Manhattan D.A.'s Office determined there was probable cause to arrest Daniel Penny and arraign him on felony charges. The investigation thus far has included numerous witness interviews, careful review of photo and video footage, and discussions with the Medical Examiner's Office. As this case proceeds, we will be constrained from speaking outside the courtroom to ensure this remains a fair and impartial matter. Jordan Neely should still be alive today, and my thoughts continue to be with his family and loved ones as they mourn his loss during this extremely painful time."
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