The reason you have to pick the pirates is simple: the pirate is goig to be at sea 95% of the time. Drunk or not, they know their ships like the backs of their weathered hands, and a ninja won’t. Sure, one or two might slip over the edge of the railing and slit a few throats, but the pirate fights on his home turf, the rocking, rolling, ship at sea, and after an initial advantage, the ninjas cannot fight back against sea-legged men with cutlasses and pistols who knife-drag their way down sails and swing from ropes like so many monkeys, kicking ninjas back into the ocean.
Where, naturally, the kraken awaits.