The killing was captured on surveillance video.
Police say Maliki Johnson, who was 15 at the time, shot and killed 27-year-old Javon Merrill inside the Triangle Deli on Ashburton Avenue last October.
Investigators believe the suspect was visiting Yonkers at the time and may have had associations with local street gangs.
They say the killing may have been the result of an earlier dispute between the victim and those same groups.
Police used DNA evidence from a piece of clothing to track down the teen, who lives in Dover.
"This tragedy highlights the urgent need to address gun violence in our cities, particularly among young people," District Attorney Miriam Rocah said. "Not only are friends and family mourning the loss of Mr. Merrill, but another young person's life has been irrevocably changed because of his own actions that day. We will continue to work with Yonkers Police and our law enforcement partners at the federal, state and local level to try and eradicate gun violence in our neighborhoods."
He was arrested last week by U.S. Marshals, brought back to Yonkers, and arraigned Tuesday on charges including second-degree murder.
He is now at a juvenile detention facility.
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