In Despicable Me 2, Edith is going through her "ninja phase" and spends most of the movie in costume. And armed.
Ninja security guards appeared in Rugrats in Paris, but it's justified, as the amusement park is run by Japanese.
The Teenage Mutant Ninja Turtles were explicitly trained by a Japanese ninja, who had moved to New York and got turned into a rat (or a rat who learned from such a ninja before passing his teachings on to the turtles). However, they are in every other way 100% American.