Difference for cruise and hotel combos -
Kenai Fjords Tours owns the Windsong Lodge which is out of town and not in walking distance to anything but they have a shuttle.
Major Marine owns Harbor 360 Hotel and Gateway Hotel which are both right in town and walking distance shops, restaurants, etc.
Major Marine is the locally owned company and has new boats on most of the tours, and uses smaller boats on the 8.5 hour.