We just returned from an Alaskan Princess cruise out of Whittier to Vancouver. We did an independent tour the week prior to the cruise in Denali and Seward with a rental car. All of it was amazing and we enjoyed everything that we did.
The ports we stopped in were Skagway, Juneau, and Ketchikan. In Skagway, we used Chilkoot Charters for the Yukon Rail and Bus tour. We took the bus to Bennett Lake and then returned by train. The cost was $184 per person and included lunch. You get to see much more than if you take the train round trip and the bus goes further into the Yukon. It was cheaper than the similar ship excursion. In Juneau, we took the blue bus to Mendenhall Glacier and then a trolley tour around Juneau. It was $45 per person and we booked independently in the port when we got off the ship. In Ketchikan, we did a private tour with another couple and used David Freeman. it was $70 per person for slightly more than 4 hours. We saw the totem parks, did a forest trail, and searched for wildlife. In Vancouver, we used Land and Sea Adventures to go to Victoria and Butchart gardens. It was $150 per person after the exchange rate.
We were happy with all the tours and found all of the providers through reviews on tripadvisor or cruise critic.