actually, teenage mutant turtles are really samurai.
umm....samurai were both good and bad....but there was no where to draw the line between good and bad, as each clan had its own views in equal extremities during the sengoku era.
there wasnt really a ruling party with established laws, just bunches of clans which were governed by the leader.
samurai could be masters of many weapons, not just katanas.
Ninjas were assasins. usually sent to kill important generals/leaders before a huge battle started with the samurai of each clan. ninjas carried next to nothing, and just used junk they found to help kill people (kitchen knives, garden tools....lol, wouldnt be suprised if they used a rock or two, and other around the house crap.)
if in the open, ninjas would be completely annihilated by mounted samurai in one run. but in close quarters like a small room, the ninja might win.
so my vote goes to samurai. because they are what shaped their era, and all of japan, while ninjas were just mere shadows. (literally, as that is what they were refered to.)