If we are being "real" then it only makes sense that the historical ninja would be fighting wokou, which are Japanese pirates of the period.

Yes, ninjas can beat Japanese pirates of that period - if for some reason the ninja's masters decide that having a bunch of pirates that mostly attack neighboring countries is a bad thing. And, if you allot enough time to mount a campaign, give them a map and an even more highly unlikely set of orders they could beat any other pirates of their time period too.