Sadly, there are no Disney films that I can think of that have a ninja in them, and I grew up watching Disney films all my life!
I think in terms of the classic Disney films, the one that comes the closest to having ninjas in it is Mulan. In this film, the warriors do learn ninja type moves, such as fighting and martial arts, but they are doing this to train to be part of an army.
Despite there being no films that contain any ninjas, there are some shows that are made by the Disney company that have ninja references:
This is a show about a young boy who is in 9th grade at school, but as well as trying to complete his schooling, he is also a ninja defeating evil.
One of the characters from Kim Possible, he was a student at a ninja school, but didn't have a very big part in the show.
Again from Kim Possible, he was the master of the ninja school, and recruited many other ninja students.
These are the main ninja references throughout shows made from Disney, there are a few others, but the shows are so obscure and the parts in them so small, they may not be worth mentioning.
Can you think of any more?