They were angry that three inmates accused of attacking a guard last week had been charged only with first-degree robbery, not attempted murder.
The funds will be limited to inmates accused of less serious, nonviolent crimes, city officials said.
Murder charges were filed today against an inmate accused of fatally stabbing a veteran corrections officer at Bayside State Prison in southern New Jersey on Wednesday, prison officials said.
The protesters were upset because three inmates accused of attacking a guard Tuesday night were not charged with attempted murder.
On July 23, Larry Davis, the inmate accused of murder and shooting six police officers, stabbed a guard with a pen in the same area as last Sunday's incident.
Peters portrays Kit Walker, an inmate accused of murdering his wife.
The Rikers Island protest began after three inmates accused of attacking Steve Narby, a correction officer, were charged last week with first-degree robbery rather than attempted murder.
Mr. Marrero said 25 inmates accused in killings were now in dormitory settings.
Of the 31 defendants, which included four inmates accused of crimes against other inmates, 22 were sentenced to death; the rest were sentenced to prison.
During the Great Purges, the prison overflowed with inmates accused of state crimes.