I am here talking about Age of Sail pirates (blunderbuss et al) and medieval Japan ninjas. No higher technology allowed.
Who wins?
Most importantly, why?
Pirates.
Because ninjas never attacked each other with lit cannon fuses in their beards. That is all.
History: So much weirder than fiction.
Edit: SIX fucking pistols. Who the hell fights with SIX pistols? That’s like straight out of Boondock Saints. Except again, not fiction.
Only one shot per pistol.
I’m aware.
That doesn’t change the fact that he had six fucking pistols strapped to his body.
Pirates; guns are a huge advantage.
Prince Rastar of Therdan does even better!
Having four arms helps, no doubt.
This Prince sounds like my kind of guy.
Ninja Pirate Zombie Robots please. And if they happen to be young adults* above the age of consent that have the hots for old ladies all the better.
*No turtles please. (Stop laughing Ben that’s not what I meant.)
Ninjas, of course, provided they have the element of surprise. They’d probably have to take the pirates while they’re in port, or at least near shore.
Otherwise, pirates.
A ninja wouldn’t operate without surprise or else he’s not a ninja.
You can’t shoot what you can’t see.
Simply being called a ninja won’t make you one. Trust me, I’ve tried. 
Also, pirates lose even harder if it’s just a one-on-one fight. Pirate will be most dead from his bread and water diet anyways, the ninja will simply be enthusiastically putting him out of his misery.
Pirates. Because they cheat.
Ninjas, being the products of feudal Japan, operated within a certain set of ‘ninja codes’. Pirates, on the other hand, just had “a set of guidelines”…
Are you kidding? Ninjas only exist because they don’t have a code of ethics or honor.
He didn’t just call himself a ninja. He was the legendary white ninja of prophecy. He could communicate telepathically with other ninjas. Do not question what you know to be true.
He could be a Hollywood Ninja.
“How can you tell he’s a Hollywood Ninja?”
“Because it’s underground, and he’s wearing all white. If it was aboveground in the snow, he’d be wearing all black.”
That’s what cannons loaded with grapeshot are for!
Ninjas.
I beg to differ…on second thought, forget the begging…I’ll just differ:
Ninjas were peasants trained how to wield modified farming instruments. They were instructed in the basics of stealth, especially concerning disguise, but in a fight mano-y-mano, they were no better than any other warrior.
Pirates were also regular schmoes, but they suffered the brutal environment of the sea. They had to worry about storms, scurvy, other pirate raids, royal navies, and Johnny Depp.
Assuming both parties are at peak condition, I give this one to the pirates. They have way more combat experience in a plain, one-on-one setting. If it’s at sea, then it’s a total slaughter.
Of course, I grant you that ninjas are way cooler, totally sweet, and will probably win this poll.
Another sensual massage, Pirate Queen?