I'm not sure if you are talking about multiple day fishing charters, or staying aboard a floating lodge style boat. I am aware of a few boats that do cruises throughout south east where fishing is done from smaller boats that cooperate from a larger boat that you stay on.
I know of.a few boats, one operates out.of.Friday Harbor, but, it's of an expedition boat, think mini cruise ship (8-10 passenger cabins) that go on expeditions up into Alaska and Canada where you sight see and fish your way north
Alternatively, up in Prince William sound there.are wanigans and that's some of.the best fishing in alaska