I just saw this so pardon me for getting in on the action a little late.
Pirates win.
Only the good pirates, though. Not the ones that are in the background just to look stupid and be killed.
Ninjas may be sneaky, but pirates can hear them. They sail all day with no sound but the sea, so their ears are finely tuned.
Ninjas can hide, but pirates can see them and smell them. They have to spot land a long way away and they know when something doesn't smell fishy.
That being said, pirates' sword skills are exceptional. No flashy, tricky moves that waste time and are very unnecessary. Pirates use brute force and just swing away, much like a Barbarian. And we all know that Barbarians own Assassins.
I have to give it to brute force. No finess players in this battle. Pirates win. The end.