Excursions can be a great opportunity for photography. However, your time is limited as you need to be back on the ship before it leaves so careful planning can go a long way. Before you get on the cruise, study maps of the area and plan. Figure out where your ship will dock at and where you can go from there. If you have activities you’ve signed up for then plan around those but understand you will likely need to meet someplace before that scheduled time.
If you aren’t registering for any guided activities have a good time but a reasonable mindset – you won’t be the only person there and may have to work around a crowd. This is doable, but you will have a less stressful time if you accept that as a foregone conclusion. Also, not every whale watch tour or bear watch tour sees bears or whales so photograph what you can get.
Finally, explore the town. Juneau had a lot of cool things to photograph both in terms of natural beauty but also in terms of manmade beauty. Meanwhile, in Skagway, I immediately hiked to the Miners Graveyard and was able to get there before the tour groups arrived – I had the waterfall to myself for about 30 minutes, that’s 30 minutes of a waterfall without another human in the way. These locations your cruise stops at have things worthy of a photo, but you have to explore for them.