How do you refer to a ship?

Currently working on a fic and I've now reached a rather irritating discussion with myself. The main character is a pirate and I'v ebegun doubting how to refer to his ship.

With a ship being considered female I've always refered to them as she/her when talking about them, the same thing my great-grandfather did (who was a lighthouse keeper and a sailor)

But how would you referer to a ship in writing? By she/her or simply it?