I'd go with ninjas because of their advancements in battle skills. In history, they were peasants who really had nothing to lose in doing these acts. Also the fact that peasants tended to farm constantly made Ninjas extremely fit, and since they were basically robbers they had to run through the forest, gaining them great endurance as well. Add that to hollywood's view of them, which is extremely sharp knives and swords, cat like reflexes, and doohickies that allowed them to walk on water; ninjas are basically unstoppable.
And to retort the "pirates have guns"
The handguns were extremely inaccurate, and took an extremely long time to reload, easily allowing any ninja to get in for the kill.
If a ninja did happen to get shot at, when using a hollywood version of ninjas, they would either dodge it or catch it.
A ninja has a katana, a weapon with great agility and rumored to be sharp enough to cut a piece of paper using only the force of gravity.
A pirate has a broadsword, which is a large cumbersome object that can easily be dodged, due to its lack of speed and agility.
The pirate, in history, were usually merchants and sailors hired by the kings of the Old World to attack and pillage other king's ships. Typically, these pirates would attack any large ship they saw, and spent the pillage as soon as they acquired it. Knowing that pirates only attack ships they saw as being bountiful, one can assume that pirates would really have no reason to attack ninjas. Add this to the idea that ninjas are stealthy and would usually work during the night, one can conclude that it would be a surprise attack on the pirates, causing lots of deaths straight off. On top of that, Pirates in history were not known to drink rum all the time, but rather they would be quite starved most of the time, unless recently in port. Pirates operated around the Caribbean and east cost of the continental US, so they would have to have traveled quite a long way in order to battle ninjas. Ninjas, typically all knowing for some reason, would get word of this ship entering, plan their attack, and get to the enemy before they could get to a safe port, seeing as pirates would not probably know where the ports are, since they did not operate in Asia. So in wrap up, it would be a surprise attack, the pirates would be famished, and it would also be night time.
But why would the ninjas attack pirates?
Remember that ninjas are peasants, and have for the most part given up on gaining any profit from their food. Now also remember that pirates would go to port whenever they pillaged a ship, so they could reap the benefits as soon as possible. Ninjas would get word of these pirates probably through traders who had seen the pirates en route, and would probably also be told that the pirates had a large cargo with them (judging by the size of the ship and its speed)
So this would make the pirates irresistible for the ninjas, and knowing ninjas, they would want to get it over with asap, thus why surprise attack at night.
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