36-year-old Eliseo Alvarez is charged with attempted assault, obstructing governmental administration, riot, attempted criminal possession of a weapon, and menacing.
27-year-old Juan Nunez is charged with obstructing governmental administration and riot.
Police say they're not looking for anybody else. The men were initially arrested for sleeping on the subway but then released with no further charges.
The Manhattan District Attorney's office said the prosecutors who declined to move forward on the sleeping-related violations were not aware the men were also allegedly involved in the altercation with the officer.
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Earlier, the head of the police union criticized the decision not to prosecute. Patrolmen's Benevolent Association's president Patrick Lynch said the men should be held accountable.
"As the District Attorney continues to decriminalize criminal behavior in the subways, we can expect to see the safety of our mass transit system deteriorate," Lynch said in a statement. "There is no telling how much damage these mopes would have done to that courageous police officer had he not been equipped to handle them. Had it gone the other way, we might have had a seriously injured or dead police officer instead. It's wrong that they were not charged for attacking him."
The video shows the officer fending off several men who appear to be ganging up on him inside the East Broadway subway station on the Lower East Side.
Police said the officer had asked the men, who appeared intoxicated, to leave the station Sunday night after a woman said they were harassing her. The men refused and then became combative, according to police.
The video shows one man charging at the officer and then falling off the platform and onto the tracks.
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At that point, the officer asked that power to the tracks to be turned off while also calling for additional units to respond.
The men were taken into custody and removed to a hospital for treatment, but no charges were immediately filed. They weren't arrested until the next morning, when police spotted them back at the East Broadway station and cited them for sleeping on the floor - a low-level violation that the Manhattan DA's office stopped prosecuting two years ago.
Prosecutors dropped that case, citing the policy curbing prosecution of those kinds of low-level violations.
"When people are arrested for attacking officers, we prosecute them," said Danny Frost, a spokesman for the DA's office. "These men were not arrested for attacking an officer, they were arrested for sleeping on the floor of a subway station - a rules violation, not a crime. We have not prosecuted this violation since March 2016 under a policy jointly established with the Police Commissioner and Mayor."
Meanwhile, Officer Syed Ali was honored for his actions inside the subway station.
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New York City Councilman Chaim Deutsch met with the officers and honored him for his restraint and discipline.
Ali, an Army veteran who served in Iraq and Afghanistan, never pulled his gun.
Mayor Bill de Blasio praised Ali's "extraordinary professionalism and bravery." He tweeted Tuesday that "attacking our men and women in uniform won't ever be tolerated."
(The Associated Press contributed to this report)
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