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My vote is for Survival. The checks for getting lost are consequences of failing Survival checks, and items like compasses and astrolabes give bonuses to Survival by default.
Just knowing how to pilot a ship doesn't necessarily mean you know where to bring it, and the pilot of a ship may not necessarily be the navigator. Although it could certainly benefit a pilot to learn navigation, it doesn't make 'any less sense' than a rogue with +30 Disable Device but only +1 Perception, who can deftly neutralize traps but can't effectively find them in the first place.
Edit: I contradict myself. Checking the Astrolabe, it grants "a +2 circumstance on Knowledge (geography) and Survival checks to navigate in the wilderness (and on Profession [sailor] checks to navigate at sea)."
Profession (Sailor), it's in Skull and Shackles, in the section under naval battles. In fact Profession (Sailor) does all of that naval/boat stuff.