You can not get the trip you are looking for on the major cruise lines. It is possible, but there ae trade-off. The Radisson Seven Seas Mariner is a high end ship where cruises start at $3,000. They do Sitka. Or you could do a custom itinerary that would include using the Alaska Marine Highway, but this would not be a cruise-based itienarary and you would not get all of the on-board activities and the unpack once and you're set for a few days experience you would get on a cruise line.