Best solution is to pre-map the ocean to the degree possible (mountains don't tend to move, at least on the timescales we care about...); this wouldn't need to be done stealthily (so you could use active sensors), and using surface ships is one option, also drone surface ships and drone underwater vehicles now. I assume there are relatively highly classified high-detail government maps of certain parts of the ocean of particular interest.

We also have highly classified models of the exact shape and mass distribution of the Earth, as this is essential to accurate long-range ballistics (i.e. for ICBMs to hit their targets) -- it affects the gravity experienced over the course, and the precision/accuracy needed is higher than just uniform-density sphere or oblate spheroid. Also of magnetic and other anomalies since that can be used as a baseline when searching for submarines or ships using magnetic sensors, although I think this is less important now.