Shea called the officers' actions "absolutely inexcusable," though he added they would not be fired or suspended.
"There is no excuse for what I saw in that video," he said. "We are better than that."
The incident happened Tuesday morning in the Greenwich Village neighborhood of Manhattan.
The video shows the maskless officers escorting the rider, identified as Andrew Gilbert, from the subway station, and you can hear the officer telling the commuter he is being disruptive.
"I've been the first to defend officers, I think many of you know that," Shea said. "I'm also the first to call out wrong when it's wrong...I think the public deserves better than that."
Gilbert sent a statement to WABC-TV telling his account of the events.
"I was just commuting to work, and when I got off the train, I noticed these two officers standing there on the platform with no masks, as is fairly typical these days for the NYPD," he said. "I've taken to filming them whenever I see them doing this in the subway, so I walked over and asked them why they weren't masked. The male officer kept pretending he couldn't hear what I was saying. He told me, 'I can't hear you through your mask,' etc. After a few seconds, another women noticed this and came over and started recording as well. She's the one who posted the video to Twitter that went viral. I kept asking them to follow the law and put a mask on, and the officer declared that I was being 'disruptive' and grabbed me and shoved me 60 feet over to the emergency exit and slammed me through it. He yelled at me, 'If you're not going to ride the train, you can leave.'"
The NYPD has not released details of what precipitated the incident, but the woman who shot the video told Eyewitness News the male officer mocked Gilbert even though she did not believe he was being aggressive or provocative in addressing the officers.
Acting New York Metropolitan Transportation Authority Chairman and CEO Janno Lieber blasted the officers and said it is past time for "more than a few cops" to start complying with mask rules underground.
"We have obviously more than a few cops that are not complying," he said. "Come on. Set an example. You are the people who are responsible for getting everyone to comply with mask wearing and with all the behavior and rules we apply to the public spaces. Come on. It's enough already."
The NYPD said the incident remains under internal review.
"I was troubled by that video," New York Mayor Bill de Blasio said. "I did not like what I saw one bit. I didn't see everything, except for the clip at the time when the person was being removed. I saw the officers not wearing their masks in the subway. That's evident. That's unacceptable. We've given this instruction 1,000 times. If you are going to be in law enforcement, you actually have to participate in following the law."
Gilbert said he doesn't expect the officers to face serious consequences.
"I sincerely hope that the two officers who assaulted me are punished as severely as the law allows, but I have no doubt that this isn't going to happen," he said. "When these officers are quietly given a slap on the wrist, it will send a message to all of the other corrupt cops out there that there are no consequences for breaking the law and abusing the public."