We usually do not book the ship's cruises because we like to explore on our own and usually walk around the towns on our own time. However, I would recommend taking the White Pass Railroad trip in Skagway if the weather is looking favorable. Since this is your father's first trip to Alaska, you might look at taking the cruise tours which give a good overview bus tour of each town.
I think that if you go to the cruise line websites, you can view the tour options at each port.

Good luck with finding some good fares. We just passed up a 7-day balcony on Princess for $599.00 each for a cruise this week.