There would be Samurai Champloo, which is an awesome fighting anime, but not necessarily with Ninjas. There are some Ninjas, but they're not the main thing. Naruto obviously has ninjas, but I doubt you're looking for that. Basilisk has ninjas. In fact, Basilisk is about two ninja clans fighting to the death.
And on an unrelated sidenote: You need to resize your signature.
The Rules say that you're allowed to have max 250 px in height, yours is 452. Please change that asap or deal with the consequences.