Out of Kodiak, Mythos Charters ran a converted fishing boat with small groups and did the total mix of things. They had a decent boat, multiple sea kayaks, fishing gear, and ran longer charters away from crowds. I am not sure if they are still doing them. The big problem is finding enough good weather to get out on the water the way you want to. You will probably lose some days, regardless...
Typical better plan would be fishing on day charters and such from a town or remotely at a lodge. There are a number of converted canneries and remote lodges that can do it for you on a daily basis. As a bonus, AK limits are based on daily limits with (generally) a two-day possession limit. The exception is that fish frozen or preserved (smoked and canned for example) do NOT count against your possession limit. Boats have trouble freezing your catch on the water...
A remote lodge I am familiar with that runs a good long-time family business is Quartz Creek Lodge on NE Arm of Uganik Bay.
http://www.quartzcreeklodge.com/They have raised a quality family there for many years and are good folks. When I go hunting in the bay they usually run out a big load of incredible tanner crabs for me. They started long before they really knew me. Good people and an amazing place. They have a couple of the best brown bear guides around in the family, too.
From Calvin's pictures and reputation, he is someone you should talk to also.