But here's a little known fact about Pirates: Pirates wore eyepatches over one eye not because they had one eye, but to cover up one from the sun. When they were capturing a ship, they would go down to the hold and switch the patch to the other eye, and they could see in the dark because of their "nightvision" eye.
Well, ninjas ftw! Pirates are dumb, sick and presumably drunk all the time. It should be clear who wins.
Ninjas have katanas, trowing stars, weapons dipped with poison, deadly acupuncture skills etc. They are fast, they have awesome agility, stealth and years and years of training.
ningas have to have some kind of boat to get to the pirate ship the guy at the top of the mast would see them tell the other pirates then the pirates would destroy them with cannons.