One victim is hospitalized with multiple injuries.
Denise Darbeau and Rachel Edwards were indicted by the same grand jury that dismissed charges against employee Rayon McIntosh in the confrontation, which was captured on video by a bystander and was posted online, the Manhattan district attorney's office said.
The charges against the women, one of whom suffered a skull fracture, won't be made public until a Jan. 11 arraignment. Their lawyer, Harold Baker, said he believed they were being charged with burglary.
"The guy that does the beating gets to walk out the door, and the people he beats end up getting charged — it seems backward to me," Baker said.
But McIntosh has said he simply defended himself after Darbeau hit him in the face and both irate women went menacingly behind the counter at a McDonald's in Manhattan's Greenwich Village on Oct. 13.
The woman, both 24, got angry when a cashier inspected a $50 bill they'd presented, a witness testified at a hearing in October. McIntosh, 31, was working as a cook that night but became enmeshed in the dispute as he took some food to the counter.
The video, shot by another customer, shows McIntosh grabbed a metal grill-cleaning tool and hit the women, even after they sank behind the counter to the floor. Darbeau was left with a fractured skull, broken arm and neurological damage, and Edwards' injuries included a serious cut to her face, Baker said.
McIntosh's lawyer, Theodore Herlich, has said the women were trying to get up and McIntosh couldn't be sure what harm they aimed to do to him. Herlich didn't immediately return a phone call Thursday evening.
McIntosh — released in March from about 11 years in prison after pleading guilty to manslaughter — initially was arrested and arraigned on felony assault and weapons charges in the McDonald's fracas. But prosecutors said Dec. 2 that the grand jury had declined to indict him on any charges.
The women, on the other hand, initially were arraigned on misdemeanor trespassing charges.
Baker said they regretted their "inappropriate behavior" at the eatery. But it doesn't compare to McIntosh's conduct, and the grand jury shouldn't have been asked to consider all three cases together, he said.
"His actions are not legally or morally justified," Baker said.
McIntosh is no longer working at the McDonald's, franchise owner Carmen Paulino said in a statement Thursday. Staffers "work hard to maintain a safe, positive restaurant environment for employees and customers," Paulino added.