With a ship, buoyancy carries the weight for free (energy wise) unlike a plane so if all you're focussed on is air pollution then ships are far better for the environment.

Well, there's this:

https://www.statista.com/chart/32350/greenhouse-gas-emissions-by-mode-of-transport/

... but a ferry is not a cruise ship.

I would imagine they would be lower on this chart than the cruise ship, cruise ships are kind of notorious amongst ship types as being just obscenely resource intensive / wasteful...

... but basically outside of WA/BC... there just aren't that many ferry systems in North America, whereas they are more common elsewhere...

Maybe there are more/better studies done in Japanese, Korean, etc, that focus on the kinds of tech and ships and fuels used in ferry systems around there?

The number you'd get out of the kind of calculation there, it could change a lot based on the overall design / route / intended speed of the ship, the kind of engine used (it could potentially have a hyrbid electrical drive system), the blend of fuel used, etc etc.

If you would be sailing, it would probably have the less impact on the environment. But a Diesel powered ferry ? I have no idea how it compares to air flight. The train is probably better than both ferry and plane in this case.

Depends how long you can hold your breath.