Ninjas don't NEED to sneak, they are just really good at it, pirates don't have super powers, aren't god, and can't bend the rules of space and time, they hang out all day on a hot ass boat, with a bunch of sweaty ass fat dudees who probably don't shower, basically they are worse than hobos.
http://en.wikipedia.org/wiki/Pirates#Life_as_a_Pirate
In the popular modern imagination, pirates of the classical period were rebellious, clever teams who operated outside the restricting bureaucracy of modern life. In reality, many pirates ate poorly, did not become fabulously wealthy, and died young.
http://en.wikipedia.org/wiki/Ninjas
Though typically classified as assassins, many of the ninja were warriors in all senses. In Hayes's book, Mystic Arts of the Ninja, Hattori Hanzo, one of the most legendary ninja, is depicted in armor similar to that of a Samurai.