It is the latest development relating to what prosecutors have called "a pervasive and deep-seated culture of violence" at what is one of the largest municipal jails in the United States.
Ronald Spear, 52, died in the early hours of December 19, 2012 after being repeatedly kicked in the head while lying face down and restrained, on the floor of a medical wing of the prison.
He had been seriously ill with kidney disease and was assaulted after getting into an expletive-fueled row with then corrections officer Brian Coll about seeing a doctor, court papers said.
The most serious charges against Coll -- obstructing justice and filing false forms -- carry a maximum sentence of 20 years in jail. Taylor also faces a 20-year sentence if convicted.
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Anthony Torres, 59, another former corrections officer at Rikers Island, has already pleaded guilty to conspiracy and filing false reports, prosecutors announced.
"Rikers inmates, although walled off from the rest of society, are not walled off from the protections of our Constitution," said US Attorney Preet Bharara in announcing the charges.
After Spear and Coll got into an argument, Coll punched him in the face then "repeatedly" kicked him in the head while he was face down on the floor and restrained, court papers said.
After kicking him, Coll allegedly picked up Spear's head and brought it just inches from his own, saying "that's what you get for fucking with me," according to court filings.
Spear later stopped breathing and was pronounced dead, despite efforts to resuscitate him.
Prosecutors say Coll continued to kick Spear in the head even after another officer told him to stop and tried to shield Spear's head.
Coll and Taylor allegedly conspired to cover up the assault.