James Kuehne stood silent at his first court appearance while his attorney pleaded not guilty to gang assault.
Police released a photo of the 31-year-old who investigators say he used his helmet to hit Alexian Lien over and over again.
"In particular, your honor, this defendant is on video having struck the defendant, I'm sorry the driver of the SUV while he's on the ground," the assistant DA said.
The suspect's family stayed silent outside the courthouse and one woman hid her face.
"He happens to be an individual who is very upset and very distraught about this case. I promise you as this case goes on we are going to have things that went on that day that are a lot different than what was shown on the video tape," his attorney said.
Roberts Sims also made his court appearance Thursday morning.
Sims, Kuehne, Craig Wright and Clint Caldwell are all accused of assaulting Lien during a road rage incident where the SUV driver hit a biker, paralyzing him.
Lien told police he feared for the safety of his wife and 2-year-old daughter.
Undercover detective Woljciech Braszczok, Reginald Chance, and Christopher Cruz also face charges, but prosecutors say they did not participate in the assault.
If the allegations are that somebody, whether it was a cop or not, tried to drag someone out of the car and beat them it's despicable," Mayor Bloomberg said.
Uniformed officers, even off duty, are expected to jump in if a crime is occurring, but rules are murkier for undercover officers, who face blowing their covers if they come forward.
Lien's wife has said he fled to protect her and their 2-year-old daughter. Lien hasn't been charged with any crime.