I'd assume features below the sea floor have a much bigger impact than surface features. Large iron deposits, volcanic activity, natural gas deposits, whatever

I'd assume features below the sea floor have a much bigger impact than surface features. Large iron deposits, volcanic activity, natural gas deposits, whatever the LLSVPs are, etc. But you could use ships to correlate gravity measurements with GPS locations and make an accurate map that way. You don't need to map the entire ocean, just enough locations to allow subs to occasionally recalibrate their position.