You all are way to fixated on ninjas. Samurai were much more deadly than ninja one on one. (<i>Shogun</i> notwithstanding, pirates really aren't even worth mentioning.) The stealth skill of a master ninja opposed to the awareness of a master samurai would be a very, very hard call to make, and I have no basis for calling it one way or the other, so surprise is a toss up. Unarmed and unarmored, their martial arts skill would also be about equal, but, on the average, the samurai would be stronger (wearing armor will do that to you). So that's an incremental advantage.
It really does come down to the kind of fight, though. In a stand up fight, an individual ninja would present a Samurai a challenge on the same order of magnitude as a daikon. In a long running feud, where all that matters is who's alive at the end, the nod oges to the ninja, but the samurai would reduce them to a lone savage hunted by all before the ninja finally garrotted the samurai on his tatami. I mean, the samurai would, if threatened, think nothing of totally depopulating the ninja's district and burning all the towns to the ground. I have no doubt that the Samurai would eventually be assassinated, but the cost would be horrible unless the ninja got very, very lucky.
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