The NYPD still has the area around East 127th Street taped off between Madison and Park avenues, guarding the bus.
The shooting happened around 4:30 p.m., and witnesses reported hearing six to eight shots, one of which hit the bus above the windshield.
The bus was carrying 11 children, mostly 5 and 6 years old, from the Choir Academy.
Police do not believe the bus was targeted, but that was little consolation to concerned parents.
"It could be my son on the same school bus, coming from school in the same situation," one area resident said. "So it's very sad to hear that, and we got to make it safe and whatever we can do."
Investigators used flashlights to search the ground and floodlights to search the bus, and another search is under way for a blue pickup truck seen fleeing the scene.
Police also found ballistic evidence around the block.
"It shouldn't have happened in the first place, that's it," resident Anthony Scott said. "I mean, there's this thing about, you don't do stuff like that. You just don't. Especially around a school. It just makes it worse. That's all. Hopefully they catch whoever it was and that will be the end of that."
Authorities say the shooting happened about one block west of where the bus was located. Anyone with information is asked to call police.