I think that the Ninjas were far deadlier. In fact they were total bad asses.

Samurais had rules-they were way cooler-Ninjas played dirty..

ninjas weren't anymore badass than samurai, not by a long shot. it takes a lot more chuzpah to duel someone head to head to the death just for the hell of it than to sneak into someone's bedroom and kill them in their sleep.
samurai > ninja.

Samurai rule!

But Ninjas understood that when it came to fighting there were no rules. You do not fight by the rules you fight to win.