The gunfire rang out just before 6:30 p.m. on the B15 bus near Lafayette and Marcus Garvey Boulevard in the Bedford-Stuyvesant section.
The 14-year-old suspect, is being identified as Kathon Anderson and is being charged as an adult with second degree murder, Criminal Possession of a Weapon and Criminal Use of a Firearm. He was arraigned Friday.
"Just going to ask everyone not to rush to judgment," said Frederic Pratt, a defense attorney.
Authorities say the suspect boarded the bus to go after a rival gang member, but instead hit 39-year-old Angel Rojas in the head.
Rojas was rushed to Woodhull Hospital, where he was pronounced dead.
The teenager was arrested at the scene while commuters scrambled to get out of the way. A firearm was recovered.
"It was chaotic," paramedic Christopher Womble said. "We arrived on the scene, people were still on the bus, people running off the bus. The gentleman was literally in the seat, not moving at all."
Police said the boy fired one shot on the bus and several more outside. Six shell casings were found at the scene. The shooting appears to be gang related, and authorites say the intended target was a member of a rival gang who had been taunting him on social media.
Girls he was with reportedly pointed out the target.
The boy has a prior arrest for an assault as a hate crime in 2011. He was charged as a minor, and the arrest is sealed.
"This once again involves crews. The stupidity of those gangs that basically, over nothing are trying to kill each other, and unfortunately in the process kill innocents. As they did with this hard working, young man trying to raise his family," Police Commissioner William Bratton said.
Rojas came to the United States four years ago from the Dominican Republic with his wife Maria and the couple's two children, 12-year-old Saury and 8-year-old Abril.
Now, the Rojas family is spending the aftermath of this tragedy in stunned grief. In a horrific coincidence, Saury was at the same hospital getting his jammed thumb checked out when his father was brought in.
"I see that my mom comes out crying, and she's was like, 'Oh, what they did to my man,'" he said. "And she come out crying, so I knew something something happened, but I didn't know what. And then I started crying. I couldn't stop crying."
They say Angel Ramos worked two jobs to make ends meet in the quest for a better life for his family.
"A good dad, a good dad that works for his family," Saury said. "He's the best dad in the world."
Saury says he can't understand why a kid so close to his own age would be involved in such a deadly shooting.
"He's too young to have a gun, and he shouldn't be with a gun at all," he said. "And why he's gotta shoot him like that? Why did it have to be my dad on the bus?"
"We learned about his family and just as everyone in New York probably feels terrible about it, we feel terrible about it too," Pratt said.