Ninjas are trained for assassination. They're good for surprise attacks and escaping. I'd also expect a ninja to be quicker on his feet.
Samurai are trained for combat. With multiple people, no less. The rigorous training of a samurai teaches him that there can be no mistakes. Every sword strike must count, and misteps will cost your life. Samurais also developed techniques to combat firearms when their era was waning.
Pirates are trained... well, they train themselves to fight as dirty as possible. Where ninjas and samurai follow codes of honor, pirates will not. However, I doubt very many pirates are expertly trained. This would be their downfall.
I would say that pirates come in at last place unless it's something like 50 to 1 (piraty strategies). Then it depends on other conditions for samurai versus ninja. What would make this even better is if you added somebody trained in a Western sword art like fencing.
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