While you're discounting self-propelled weapon systems like torpedoes, I prefer a similar solution. Think in terms of remotely operated vehicles used in warfare today, or think of it in terms of an aircraft carrier with squadrons of 'intelligent robot submarines'.
I'm no physicist, you'd need someone like Torstan, or some willing to Google-fu it. Sonic is probably more effective, but how is focused sonic attacks affected by hydrodynamics (does the sound just spread anyway?) - I can't say. Your other options may or may not be effective either, I don't know.
I like 'intelligent robot submarine bombs'!