Well it would really depend on the ninja's skills wouldn't it? You see, the samurai is heavily armoured, and therefore, protected. However, popular belief says that ninjas are expert fighters, and so maybe don't even need armour. If both subjects had equal skills, then the samurai would have the better chance because of his protection. Yet, one might believe that the ninja, is in fact, quite stupid if he is to turn up to a fight with no means of protection at all... but both subjects would have learned several different styles of martial arts, so then it comes straight back to skill again.