Silent Swords is nice... at first i was hesiteting because the screenshots didn't look so good, but finally I bought it and I'm happy!
I would say..Samurai: Way of the Warrior. Its not ninja, but it came to mind when I saw your thread. I love that game personally, its maintained a solid spot on my 2nd page. It has really a really cool art style, and the gesture system is pretty fun. I think its worth checking out.