If you want to hike, you definately want to go independent, NONE of the tours have more than an hour at Mendenhall and usually less time. Just take the shuttle bus $12 round trip pp. The Gold Creek Salmon bake is good, and they run a continous loop bus from the dock area.
But I give an edge for my preferences to the Thane Ore House for salmon, reservations are needed and they shuttle you back and forth. Right at the dock near the tram is Twisted Fish, another good choice.