The vehicles collided at Glenmore Avenue and Warwick Street in the East New York section just after 7:40 a.m.
Five people on the bus were being treated from the mini bus, which was carrying special needs children.
The motorcycle ended up under the bus.
The riders, a 50-year-old man and his 7-year-old daughter, was taken to Brookdale University Hospital in stable condition.
No one on the bus was taken to the hospital, and all evaluated at the scene and treated for minor injuries.