I'm sure he was referring to the Piratians calling them skull pirates, just giving him crap about it. They're from Oracle of Seasons and Oracle of Ages. In Ages, the captain is part of the impetus for the entire conceit of the story so they're kind of important too the story. They also show up...
I refuse to participate because the best Zelda pirates aren't even included in the poll! The Piratians are the piratiest pirates in the entire series, and I'm repping them hard.