I have fortunately had some great fishing and rough water experience in both the 24' Sea Sport and the 22' C-Dory up here. On the Sea Sport side:
Great number of the Charter Captains up here use Sea Sports. They are comfortable at speed getting the clients out to the Kings and Butts. They fish well, they are quiet, they are well built, the interior's are well thought out, they are easy to clean up, easy to add poles, downriggers, towers, kickers, electronics, they hold up well to the rough conditions, pretty easy to maintain and pretty easy to re-engine. The main engine size tends to be at least a 350 and the Volvo DuoProp outdrive is preferred. The clients appreciate the boat and believe it to be a "Professional Rig". When the clients have caught their limit, or they are just plain tired, you can do about 25 to 35 mph back to the dock, even in the rough stuff and the banging is not too scary. There is lots of room to put things, even a bunch of fat and sassy Kings.
They are heavier, the 350 with DuoProp consumes about 3 times the fuel as a C-Dory, they require a more heavy duty trailer and a stronger rig to tow and stop them. When you are out trolling or mooching in the rough stuff, that back cockpit area is cluttered due to the inboard location of the engine and the engine cover that sticks out about 3 feet by 2 feet by perhaps 1 foot tall. This can be a bit hazardous along with the feeling that you are standing a foot or so above the water and you get thrown about a bit easier. You have to step down to get into the cabin and when it is rough you tend to want to stay just exactly where you are planted due to your uneasiness of moving about.
There are several Charter facilities in other parts of Alaska that use C-Dorys but from what I have heard, these locations are in quieter waters. I know of no C-Dorys that are used as Charter in the Sitka area. There are however quite a few C-Dorys in use by the locals for just about everything else. Many of these are early models and most of those are not well cared for or babied, but they are still in good condition despite the neglect. Fishing in the rough stuff up here seems more comfortable and safe (at least in the 22) due to the lower stance. The cockpit is clean and easy to move around in when you have something fighting their way all around down below. Leaning out with a net or club feels safer and it is easier to leverage yourself against the side. Probably less of a lift to get that 50 pound King in the boat. The gas mileage is noticeably better, the boat is easier to trailer, launch and store. If you are as fanatical about clean tanks, it is much easier to yank the tanks every year and clean them out; it is easier to get in and out of when it is on the trailer as well. When it is rough you still feel safe walking all over the boat, although the water seems a lot closer to you. They, like the Sea Sport are easy to maintain, although an engine problem is a bit more difficult to get to, a fouled prop seems easier. They are reasonably easy to clean, but only if they are out of the water as you cannot wash the blood out as easily if it is in the water due to the lack of self draining.
The C-Dory is noisier, they bang in rough water and when you hit a big wave the boat seems to flex more and you "feel" it in your inner ear due to the cabin air pressure I presume. The cabin seems a little narrower but the view seems more accessible. The cabin roof is not as thick so mounting things to it takes more caution and it probably supports less weight. I would not feel as comfortable with four fishermen aboard in the 22' as I would in the Sea Sport 24' but I would much rather camp out with four in the C-Dory than the Sea Sport. I have yet to see a Sea Sport with a "Camper Back" canopy up here, but that may be due to the support bars getting in the way of fighting fish.
As to which boat I would buy, that is a tough decision. Both boats are excellent tools, well build and well respected. I will point out though, as far as I am aware, there are few Sea Sport fanatics and I don't think they have a fan web site like the C-Dory has. Never underestimate a product that has a huge following, usually there is a reason for such passion!