I cruised last year - Sept. 1-8. Here is a link to my trip report:
http://www.disboards.com/threads/a-...ce-alaska-sept-1-7-photo-links-fixed.3333646/
We had great weather, awesome excursions, and it was one of the best weeks of our life! As has already been mentioned, you will not be disappointed in a whale watching excursion. I recommend going on a smaller vessel though. Another passenger on our cruise went on a disney chartered whale watching tour, and the boat was so full she couldn't even get her camera out to snap any shots. She was very disappointed. I recommend Harv and Marv's whale watching tour. They have small boats and you get up close and personal views. We had the best time! Saw breaches and spy hopping. It was absolutely amazing. I can't recommend that excursion enough. My trip report has a link to a video that our captain took on that tour. You can see me in that video...long hair and black jacket. It is worth the watch.
The whale was hopping up and down right next to our boat. It was so cool!
In Skagway we opted to skip the train. There were mixed reviews on how boring it was etc... and for the cost I just decided on a cheaper option. We booked Dyea Dave. He has a small locally owned company that takes bus tours up into the yukon. You follow the same route as the train, except in a small bus. The windows are huge so you can get great pictures on the way there and back, and they will stop any time you want to for the most part. We had tons of picture stops. They have a website you can check out as well. Google will get you there. For the two of us it was close enough to a car rental price that we chose the tour. If we had our kids with us, a car rental would have been a cheaper option. I was trying to save money however I could. All the amazing ports of call add up when you want to do an excursion in each one.
We also did the Deadliest Catch Aleutian Ballad tour in Ketchikan. It was fun...very educational. Kids would love this tour. As a bonus we even saw a whale on this excursion. Kind of expensive for what it is...but I don't regret it.
I only wish we could have afforded an excursion to see bears. One of our table mates booked a bear watching excursion...and they didn't see one bear. So, that made me feel better that I didn't put down the money on that. The bear viewing excursions were expensive from what I could find. Maybe the right time of year isn't early Sept. to see bears.
Have fun! I think no matter what you do, this will be an AMAZING cruise. I loved every second of it! We saw dahl porpoises from the deck of the ship. Many people saw whales, but we never did...so I was really glad we booked the whale watching tour. I wish we'd seen some orcas...but they were hiding that week.
You will love it!