the ferry and the hideout are both underneath that central rock formation,
that is also "the portal to SoT from the real world".
You can also hear cannon shots, when you are on the ferry.
Using a good headset you can clearly hear the cannon shots are above your position.
You can even see the actual ferry from above, when you go to that rock
and try to get that graphical glitch, where everything underwater is bright white
for a short time. (you get this when you switch between underwater and above water view)
Another easy way to confirm the location of both the ferry and the hideout:
- wait for active skull fort (and remember where it is located)
- go to the ferry or the hideout and then return
- as soon as you are back out of the loading screen: look to the skull fort / cloud
the cloud will still be looking away from you to the centre of the map
because it is always looking at you, even when you are in the hideout or on the ferry
You can actually see it slowly turning back to you after the loading screen
This works best if you enter the ferry/hideout from a position that is NOT in
line of sight with the centre of the map AND the skull cloud.
Try to make the skull cloud turn 90 degrees in relation to map centre and your
"after loading screen position" for best results.
edit: ferry of the damned location and how to find it: