Cross Dressing Predicament

I am not entirely sure this is the right place to ask this question but hopefully someone can help me out. Currently I am writing a novel about a girl who cross dresses so that she can live on a pirate ship. My problem is that I am telling the story from the two main character's perspectives, and I am not sure when to call her a her and when to call her a him. Here is a small excerpt to show you what I mean.

“I thought you might be hungry.” Jo explained, balancing the tray on the chest at the far end of the cabin. Jo pulled a shiny green apple out of her pocket. “Unfortunately, all I can offer you is some hard tack and grog. But I was able to sneak an apple.”
Willelm took a bite of the tart apple, watching Jo balance himself in one of the hammocks. “Why are you being so kind to me?”

Should I refer to her as a her when I am telling the story from Jo's perspective and then call her a him when I tell it from Willelm's perspective? Or should I keep it consistent and call her a her throughout the story, even if the other character's aren't aware of her true sex? Thank you for your help.

I'd say that since she is a girl, I'd have it as her (unless someone is referring to her in dialogue or thought, then they would use him). Since the reader knows that she is female, it should be okay. So long as there is a clear distinction on who knows she is female and who thinks she is male.

Well, what point of view are you using to tell the story? If it's third-omniscient, then refer to her as a she. If it's third-limited, depending on how limited the point of view is, having it vary based on the character we are following makes sense.

I suggest looking at how many times you jump viewpoints in a scene. If it is a lot, then referring to the character as a she would be less confusing since you'll be closer to the omniscient side of third-person. If you follow only one character's viewpoint at a time in each scene, then you're closer to the limited, almost-first-person side, and so switching genders between viewpoints would make the most sense. It will also add more impact to the reveal, if there is a reveal.

Should I refer to her as a her when I am telling the story from Jo's perspective and then call her a him when I tell it from Willelm's perspective?

Do it that way.

My first instinct is what Lauren said, but Kyllo's got some good advice too concerning the different PoVs. *unhelpful*

Just refer to her as a female, otherwise the readers will get confused. As Lauren2010 said, just make sure to clearly show whether characters know she is female or not (as long as they don't catch her in the shower, they shouldn't know...).