He was identified at a Friday afternoon press conference as 15-year-old Matthew Godwin.
He was arrested at around 2 a.m. inside the lobby of the 95 Hotel on Third Avenue in the Bronx, where police say he was sent by his mother to avoid arrest.
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He is charged with murder, manslaughter and two counts of criminal possession of a weapon.
At the same news briefing, police identified 18-year-old Omar Bojang as the suspect for whom they are still searching, who they believe was driving the scooter from which the fatal shot was fired.
Bojang has been shot twice in the past, police said, and has prior arrests for gun possession and is also wanted for robbery.
The intended target of the shooting is also believed to have been a teen who was not hit, but the bullet traveled a half block and struck Tay.
She went into a nail salon for help and collapsed before later dying at the hospital.
Her father, Sokpini Tay, gave a tearful plea at a rally on Wednesday.
"Please have mercy for her," he said while crying. "Please don't forget her. Please. She's a baby. She wasn't grown up yet. She didn't have time to grow up. I'll never get a chance to see her again."
Public Advocate Jumaane Williams was joined by Bronx Borough President Vanessa Gibson, City Council Member Rafael Salamanca, District Attorney Darcel Clark, and advocates at the "Justice for Kyhara Tay" rally to call for resources, support, and change.
"To the community, if you know who these people are, say something," Clark said. "This is our job. This is our community. We've got to flip the script on them."
According to the NYPD, there have been 65 shootings, three of them fatal, with victims under 18 so far this year.
Grief counselors are at Bronx Academy for Multi-Media, where Tay was a sixth grade student as classmates mourned the loss of a friend.
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