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As seen for the anime standpoint. Let's examine our main characters.
One Piece: Monkey T. Luffy.
Pros: Streching powers, captain of ship. Cons: Inabilty to swim, annoying tendicies, laughs at inappropriate times, obsession with a straw hat.
Naruto/Naruto Shippuuden: Uzumaki Naruto
Pros: has demon sealed inside him which offers a large variety of abilities both superhuman and supernatural. Can walk on water. His jutsu include the Rasengan, Kage Bunshin, Summoning. He is a member of a large village of elite ninja with abilites equal and greater to that of his own. This abilties can range from turning invisible to cutting a waterfall in half. Cons: Due to a badly done translation, has the irritating catch phrase "Believe it!" in the English anime. Some comedic relief can be childish or irrelevent to American viewers.
Based on this, I will have to rule in favor of ninjas. I will further update, using several different mediums as evidence.