Michael Lopez, 27, is facing attempted murder, assault, reckless endangerment, and weapons charges, and further charges are expected.
Officials say Lopez was arrested Friday morning at a step father's house in Harlem.
The suspect was arraigned on Saturday.
"It took days for the suspect to be apprehended. But what we really needed was for the public to come to us immediately to let us know who the suspect was, so that we could get him off the streets as soon as possible," Bronx District Attorney Darcel Clark said.
Sources say Lopez was once arrested for shooting and nearly killing a man but escaped the most serious charges.
That was in 2014. He was later convicted of attempted assault and conspiracy and served just two years in state prison before he was released on parole in 2017.
He has a total of 12 prior arrests, including a knifepoint robbery in the transit system just last year.
"How does an individual, released to parole, get arrested for knifepoint robbery and is walking around on the streets?" NYPD Commissioner Dermot Shea said. "And is that justice for those little kids? So I would ask, where are the laws for those kids? Because somehow they've been forgotten in this."
If convicted, Lopez faces a max sentence of up to 25 years in prison.
Police say they are still looking for the suspect's accomplice.
The original incident was reported around 6:45 p.m. on Thursday in front of 1551 Sheridan Ave.
The children, a 10-year-old girl and her 5-year-old brother, somehow avoided being shot as the gunman fired multiple shots on his intended target, a 24-year-old man.
The suspect fired about a dozen shots in total.
The victim was shot three times -- once in each leg and in the lower back -- and taken to the hospital, where he is expected to survive.
The children were not physically injured.
WARNING: The following video is shocking -- everyone involved survived
After the shooting, the suspect got on a scooter with a second person and they both got away northbound on Sheridan Avenue.
NYPD Chief of Department Rodney Harrison said the shooting "seems like it's a gang incident, which has been plaguing NYC this year."
"I'm disgusted, I'm going to be honest with you, it's very alarming," Harrison said.
Anyone with information is asked to call the NYPD's Crime Stoppers Hotline at 1-800-577-TIPS (8477) or for Spanish, 1-888-57-PISTA (74782).
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