Both boats are overkill for cruising the San Juans to Southeast Alaska. I've done the whole thing, including around Vancouver Island, in a C-Dory 22 and a bunch of times in a Nordic Tug 37. For running around the San Juans, the smaller boats are faster, easier to care for, and easier to get into transient moorage.
We found the interior layouts of the Nordhavn 40 and 43 a little tight and their cruise speeds a little slow. For similar money to a 43, we bought a Nordhavn 50 that is much faster (can cruise 8-9 knots all day) and more spacious, but older.
The only reason I sold my Nordic Tug and bought the Nordhavn is because we plan to do more offshore travel and possibly cross the Pacific. If we weren't planning to cruise beyond the Inside Passage, we would have kept the Nordic Tug or perhaps moved up to a larger model for more room and amenities. I felt the tradeoff of higher speed capability, larger windows, more open spaces, and simpler systems for less seaworthiness, range, and redundancy was a pretty good one for Inside Passage travel.
We really do like the Nordhavn. At anchor it's much quieter and has a slower, more comfortable motion. Underway, active fin stabilizers and a ballasted full displacement hull make conditions that had lockers flying open on the Nordic Tug totally benign. But it's a whole lot more to learn, which I enjoy, but not everyone does.
One small example. My Nordhavn fuel manifold has 20+ valves, which allows any combination of supply, return, and polishing that you could dream of, including many that will shut down or even damage an engine. The Nordic Tug had just a few fuel valves. In 4000 hours of operation I never touched them except during the annual Racor filter swap. With a load of bad fuel the simple Nordic Tug design would be more challenging to deal with (no way to polish or isolate), but that never happened.