Pirates are the Flying Spaghetti Monster's chosen people. Being holy they are therefore infinitely greater than those evil sneaky ninjas. Besides if the ninjas got on a ship to fight the pirates they would get sea-sick and the pirates would blast the bejeezus out of them with their cannons, ninja bits would pepper the sea as they are cruelly slaughtered. Regardless of a ninja's swiftness, they can't dodge a pistol shot, and pirates would pwn their pansy katanas with cutlasses and extreme 1-1 sword skill, plus drunken rage.
Ninja's are SO AWSOME pirates are just crepy ninja's are Smarter Faster Stronger Better equiped More balenced Skilled Trained Healthier Pirates are fat lazy drunk guys, so ninja's are WAY BETTER.
I think that a SPARTAN could kick both a pirate AND a ninja's butt at the same time. SPARTANS are so much cooler. Think about it, they have awesome throwing spears, they have amazing close range swords, they have HUGE sheild, and to top it all off, they are extremely strong.