Anthony Logan, 23, of 535 Mumford St., faces one count of first-degree reckless endangerment, a felony.
He also faces three misdemeanor menacing counts, accused of threatening three officers during the confrontation.
Police fired multiple rounds at Logan Monday morning as he stood on the second-floor porch of 535 Mumford St. Police said he told them he had a gun and then swung his arm toward them while holding an unknown object, according to court documents.
Police have since determined Logan did not have a gun during the confrontation.
Logan's actions put officers "in fear of their own lives and the lives of pedestrians in the area and (forced) officers to fire numerous rounds while in a crowded residential neighborhood," the charging paperwork states.
Police hit Logan with two shots, one in the shoulder and one in the hip, police said. He is recovering from the wounds at Albany Medical Center.
Logan was arraigned on the charges Thursday afternoon in his hospital room, attorneys said.
Judge Matthew Sypniewski, defense attorney Brendan Keller and Assistant District Attorney Stephanie Hughes traveled to the hospital to hold the arraignment. Logan is under guard at the facility, held on the new charges and on a violation of his parole in a 2012 Schenectady gun case.
The judge advised Logan of his rights and entered a formal not guilty pleas on his behalf, Hughes said. The judge also made sure Logan understood the proceedings before going forward.
Police have not identified the officers who fired, indicated how many fired or how many shots were fired, citing the ongoing investigation. Evidence visible at the scene this week suggested at there were at least six bullet holes and possibly more.
Court paperwork accuses Logan of menacing three three officers at the scene -- Jonathan Haigh, Nicholas Mannix and Craig Comley -- by pointing an unknown object in their direction, leading to the shots being fired.
Logan also faces charges stemming from the domestic dispute that prompted the initial police response to the home.
He's charged with unlawful imprisonment, a felony, for keeping his wife in the home and choking her, according to court documents.
He also faces misdemeanor counts of criminal obstruction of breathing and criminal mischief for allegedly prevented his wife from calling police.
No charges have been filed yet related to a sawed-off rifle and ammunition in a bag police said they saw Logan toss to a neighboring building shortly after they arrived at the scene. Officers quickly recovered the bag and knew of its contents prior to the shooting, police said.
Prosecutors are researching how the altered rifle fits into state and federal statutes, District Attorney Robert Carney said. For now, it appears it would fit into state statute, but it could also go federal. A decision is expected later, he said.
A bystander captured the police shooting on Facebook Live and police microphones and in-cameras are also believed to have captured parts of the incident.
Police Chief Eric Clifford, at a Wednesday press conference, said the investigation continues, but evidence, including the Facebook Live video, indicates to him that officers were justified in their actions.
Carney said his office will review the police findings, once the investigation is complete.
The New York Civil Liberties Union issued a statement Thursday indicating they are monitoring the case.
"This very serious incident raises questions that deserve a thorough, fair and transparent investigation," the NYCLU statement reads. "We will be watching what happens next."