This is probably getting into the realm of conspiracy theory now, but what better than to disguise a submarine to make it sound like a whale, and moreover convince everyone else that it is? Of course if it is actually some highly classified stealth submarine, we may never know...
It somewhat reminds me of this: https://en.wikipedia.org/wiki/Peryton_(astronomy)
Given the range over which it operates and how long it has been doing so and the fact that no one has admitted it is one of theirs suggests if it is a submarine, it is one from a major military. Those put considerable resources into making it hard to hear their submarines. This thing is way too easy to hear, which probably rules out submarines.
And if you're trying to be all conspiratorial about it and suggest it's a submarine... well, how about making the submarine sound like a normal whale first.
Seaman Jones: [teaching Beaumont] Hear it now?
Beaumont: [resigned] No.
Seaman Jones: Beaumont, at Caltech we used to do this in our sleep! You hear it now?
Beaumont: Wait a minute...
Seaman Jones: Uh oh...
Beaumont: Buried in the surface clutter...
Seaman Jones: Yeeeesssss?
Beaumont: I should go to SAPS?
Seaman Jones: Correct! Seaman Beaumont, Signal Algorithmic Processing System. Give it a week and you'll be teaching at Caltech. So, like Beethoven on the computer, you have labored to produce... [dot matrix printer rattles] ...a biologic.
Beaumont: A what?
Seaman Jones: A whale, Seaman Beaumont, a whale. A marine mammal that knows a hell of a lot more about sonar, than you do.