We did the tour through Sourdough Tours that included both of them. It ended up being a wonderful excursion -- our family of 4, and 2 other ladies from our ship. The driver was excellent and gave us a very good tour of Ketchikan -- taking the time to point out a couple of different spots where we could see Bald Eagles and actually drove us through a residential neighborhood to show us some beautiful flowers in front of his house. The tour also included a trip to "Dolly's House" and then we had time to shop our way back to the ship.
If I had to pick a favorite between the two locations, it would have been Totem Bight. It's located right on the water and the scenery was gorgeous. If you go on the ship's tour to Saxman Village, it includes admission to the native dancers and a tour of the carving shed, but the independent tours don't.