I am not familiar with cruise lines, per se.
However, you might really enjoy traveling on the Alaska State ferry system, known as the ALASKA MARINE HIGHWAY.
Read here for lots of useful routing information: http://www.dot.state.ak.us/amhs/routes.shtml
It is possible to book cabins on the larger ships. Adventurous souls sleep out on the deck of the "blue canoes" as they make their way from small port to small port. Passengers can either sleep in their tents or in sleeping bags on lounge chairs under heated covers on the upper decks.
There is nothing quite like awakening at 1am on an Alaskan summer night to see the Inside Passage sliding past in the evening light.
On the Alaska Marine Highway, you will meet lots of students going to work in the canneries, resident Alaskans traveling across the State, retirees who love the outdoors, and travelers from all points of the Globe.
The north and southbound intineraries of the Inside Passage stop at slightly different ports-of-call. They are all interesting.
The routing that works for you depends on your dates of travel and entry points more than the on the ship's itinerary.
Do not limit your thinking to only southeastern Alaska. The sailings along the ALEUTIAN ISLANDS and to KODIAK ISLAND are also worthwhile.
You should also consider a visit for kayaking and. camping in GLACIER BAY NATIONAL PARK. http://www.nps.gov/glba/planyourvisit/index.htm
Look into an extension of your trip to DENALI NATIONAL PARK for hiking and wildlife viewing.
Check out the ALASKA PASS, a product that allows you to combine various forms of transport to create your own independent Alaskan vacation: http://alaskapass.com/itineraries/
For the land portion of your trip, you can find BED and BREAKFASTS. The Alaskan summer season is short. The BnBs fill up fast ,so book early. Here is one site for Alaskan bnbs: http://www.alaskabba.com/