I haven't seen the show.
At any rate, "fanboyism" aside, ninjas win a 1 on 1, pirates would most likely win an all out "war". Because that's what they did. Ninjas were trained to be spies: assassinate silently, poison, steal. They weren't magic fighters that could take on hoards alone and they certainly had nothing to do with what you see in Naruto. But they were extensively trained to take on ANYONE and even uneven odds. So 1 on 1, or 1 on 2-3, ninjas probably would win.
Pirates, on the other hand, as seemingly disorganized as they were, they all knew their place in an all out war, that's what they did. Ninjas weren't trained to fight open wars. Off course they knew their way around a sword and bow, and they'd still kick your ass in any terrain or scenario, but all out open wars weren't their field, they were more individualized and lacked the structural organization the pirates had. The pirates, while less individually "developed", were best prepared to fight as a group.
But the fight itself is ridiculous as you're comparing 2 completely different units with 2 completely different purposes... Would be like pitching the CIA secret OPs vs the Marines.