Unless I am wrong ninja were the not so honor bound samurai that specialized on sneaking and spying, they were more often than not despised, although clans used them to do what the regular samurais would never...
Of course that comes from some not so precise information, like a few books and a japanese friend who has been champion of the south america championship of Kendo... he has a lot of knowledge about oriental samurais and the like and first hand experience with swords, not to say that he is playing in my current Midnight group...
But it may wrong, although it is very very generic to actually be so wrong. Other than that, there is too many modern ocidental myths around the ninja.