As to the efficiency of the permanent magnet versus the field wound motor I would suppose the wound motor may edge ahead as the better. Turning a large prop slower is going to produce better efficiency at low speeds than the smaller fast turning prop. However as speeds increase the small prop will gain the advantage. It would also seem that any reduction is going to reduce the overall efficiency of the system. Noise from either is probably more a factor of how well the units are designed and installed than the difference between the inboard and underwater motors.
Submersibles are consistently quiet.
I have built some 80 boats all powered with submersible motors. I have never used the inboard configuration, though I have seen many. I am sure to be biased toward the submersible. As time passes submersibles get more and more powerful. This motor is enough to push four people about in a well designed boat at 6 miles an hour or so.