Mr Penny, a former US Marine, is accused of putting 30-year-old Jordan Neely into a chokehold after he became abusive towards passengers.
Neely, a Black man, died soon after the May incident and his death was ruled a homicide by the medical examiner.
A grand jury indicted Mr Penny, who is white, on charges of manslaughter and criminally negligent homicide in June and he has pleaded not guilty.
Lawyers for Mr Penny filed a motion to dismiss the charges in which they cite testimony from witnesses in the subway train during the incident.
According to court papers, one person testified that they thought they were “going to die” and described the incident as “absolutely traumatizing.”
Another witness stated that she hid behind her stroller with her son to get away from Neely who she said was making “half-lunge movements” and was within “half a foot of people.”
After the incident, Mr Penny reportedly told investigators that he used the chokehold because Neely was in an “irate” state.
Mr Penny is due back in court in December.