Ramsey's actions come after federal and local law enforcement officials declined to bring criminal charges against the officers.
Federal authorities spent four years investigating allegations of falsified warrants and thefts from bodegas, and in March 2013, declined to file criminal charges. The U.S. Attorney's Office cited a lack of evidence and problems with witnesses' credibility.
After it became clear that no criminal charges would be filed in connection with the alleged thefts and falsified warrants, the department began an internal investigation to see whether the officers had violated department policy. That inquiry, which concluded last month, sustained eight findings of misconduct against the squad.
Ramsey said he took into account "the seriousness of the accusations" and also the time that had elapsed.
"This is a black mark on the department," he said. He stressed that the wrongdoing did not reflect on the "overwhelming majority of officers" on the force, but rather on "a few who lost sight of the values of the department."
Cujdik, a 17-year veteran and the scandal's most public face, will receive the most severe punishment.
Two other officers were suspended for 30 days, the harshest punishment Ramsey could levy other than termination, he said. Another officer and a supervisor also face suspensions.
Efforts to reach Cujdik and the other officers were unsuccessful Monday. John McNesby, president of Lodge 5 of the Fraternal Order of Police, said, "We are aware of the pending discipline and will be speaking to the commissioner in the coming days."
Tolstoy will be suspended for 30 days for giving gifts to informants and lying to investigators about it, Ramsey said. Tolstoy could not be reached for comment.
The District Attorney's Office is reviewing two sexual assault allegations against Tolstoy. Ramsey said Monday that the officer would not return to street duty while that investigation is pending.
The department investigated three allegations by women who said Tolstoy sexually assaulted them during drug raids. In two of those cases, Ramsey said, Internal Affairs found insufficient evidence to support the women's accounts.
In the third case, which was reviewed by a federal grand jury, DNA evidence did not match Tolstoy, the commissioner said.
Officer Robert McDonnell will be suspended for 30 days and transferred to a different squad for fabricating evidence on a search warrant, Ramsey said.
Officer Richard Cujdik, Jeffrey Cujdik's brother, will be suspended for two days and transferred to another squad for searching a bodega owner's van without a warrant, he said. His supervisor at the time, Capt. Joseph Bologna, will be suspended for three days for failure to properly supervise.
Jeffrey Cujdik's misconduct was the most extensive and thus his punishment the most severe, Ramsey said.
According to people familiar with the inquiry, investigators found that Jeffrey Cujdik and McDonnell intentionally fabricated evidence on one warrant.
Investigators say they believe Jeffrey Cujdik often attributed buys to an informant who was renting a house from him so he could use his reward money to pay rent. The department found Cujdik had violated guidelines by allowing the informant to live in his house, and cited Cujdik for lying about it.
Internal Affairs investigators also found that Cujdik and Tolstoy gave informants cigarettes, money, cellphones, and prepaid phone cards, sources said.
One informant called Cujdik a "true friend" who had made several small loans to the informant's girlfriend, according to investigators.
Another informant said Cujdik have him clothing, alcohol, and money for cases he had not worked on, investigators said.
A third informant said Cujdik gave her mother $300 to bail her out of jail, sources said.
The investigators concluded that both officers lied when asked about the gift-giving.
Richard Cujdik admitted to investigators that he had searched a van without a warrant in the raid of a bodega. The department cited Bologna for failing to supervise him.
One bodega owner captured video of the officers cutting wires to security cameras during a raid, according to sources. Bologna, the supervisor, told investigators the camera was dismantled for safety reasons - to protect plainclothes officers' identities.
The cameras were seized as evidence and placed on a property receipt - standard procedure, the officers told investigators.
There was no department policy at the time on dismantling security cameras, so investigators concluded the officers had not violated any departmental policies. Investigators did, however, recommend that the department establish a clear policy on such practices.