David Davon-Bonilla was arraigned Monday night and was held without bail.
His accomplice, Leovando Moreno, also pleaded not guilty and was held on $20,000 cash bail. He has an outstanding warrant for public lewdness in Seaside Heights, New Jersey, from an Aug. 2022 incident.
Both men have return dates for court Friday.
Davon-Bonilla crossed the U.S. border at Eagle Pass, Texas, on Dec. 7 2022. He told Border Patrol he was en route to Miami, but instead went to NYC.
On April 3, 2023, Davon-Bonilla sexually assaulted a 34-year-old woman while staying at a hotel-turned-shelter in Gowanus, Brooklyn.
In June, he pleaded guilty to assault in the second degree after the victim said she did not want to testify. He had been held at Rikers Island since the arrest, so he was granted credit for time served behind bars and released June 24.
"After he spent over a year in jail and following the victim's request not to testify in any court proceedings, this defendant was offered a plea of time served and court-managed programming," the district attorneys office said.
Mayor Eric Adams called the suspected rapist "the poster child of what's wrong" with the city not coordinating with federal immigration agents on deportations.
He called the attack "a really despicable act," and reiterated that he believes the city should be able to communicate with ICE to remove the most violent migrants.
"As you know, laws do not allow us to coordinate with ICE, that's the law, I'm not happy about that," Adams said.
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Video shows 95-year-old grandmother assaulted by home aide in Harlem
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