Authorities say 26-year-old Clive Rosario, a Level 3 sex offender, was taken into custody by detectives.
Surveillance showed the suspect walking into a building in the Parkchester section Monday.
Police say Rosario followed the 14-year-old victim into the building, spoke to him briefly, then sexually assaulted him.
Rosario, who was only recently released from prison, is charged with criminal sex act and sexual abuse.
He was previously behind bars for sexually assaulting two boys, ages 12 and 15, in Manhattan in 2004.