We did our Alaska trip on the Sun two years ago. It was a slightly different itinerary, since we left from Vancouver, but I'll be glad to share what we did, since 3 of the ports are the same. We went to Wrangell instead of whatever Canadian city she's stopping at this year, but that's the only difference.
It really depends on what you want to do. We went for my daughter's HS graduation present -- and didn't really plan on doing it until about 3 months before we left. We hadn't allowed ourselves enough time to save the money for any of the helicopter/plane ride excursions, so we didn't bother with them. If you want to do a glacier landing or dog sled trip, it will definitely be lots of $$$$$.
In Ketchikan, we arranged an independent tour of both Saxman Village and Totem Bight through Sourdough Tours. I think it was about $30 pp, and was well worth the money. Our tour guide was great. He was a native of Ketchikan, and had wonderful insights into the community. It also included a tour of Dolly's House on Creek Street.
Juneau was our only really expensive excursion, which was the Tracy Arm Fjord/Sawyer Glacier catamaran excursion, booked through NCL. I recommend this one extremely highly. It was expensive (somewhere around $150 pp), but we saw whales, excellent scenery, both North and South Sawyer Glacier, and tons of seals on the icebergs in front of South Sawyer Glacier. They go there to give birth, and there were literally hundreds of them. We were able to see both glaciers, where as the ship was iced out of North Sawyer glacier, and the passengers on the ship had a much more distant view of South Sawyer than we did. This can only be booked through NCL, as you actually tender back onto the ship where it stops to view the glacier.
One word of caution -- getting within viewing distance of the glaciers is NOT guaranteed. It depends on the weather conditions. If there is too much ice, you won't get there. It also depends on the amount of daylight, as the ship has to be out of the fjord before dark. So far, none of the sailing this year have made it to the glacier, but it's still early in the season.
We had also planned on taking the Mt. Roberts tram in Juneau in the morning, but it was too foggy to be worth it. We ended up catching a tour bus over to Mendenhall Glacier. I'd also recommend getting to Mendenhall Glacier, as it will be your best 100% chance of seeing a glacier unless you're doing a glacier landing.
In Skagway, we rented a car and drove to Emerald Lake. The car rental was about $80 for the day, as compared to the train ride which was $90 per person. My kids weren't particularly interested in the train, so we didn't want to spend that much on the White Pass train excursion. Next time, I'd like to do that one.
Have a wonderful cruise. We loved the Sun and can't wait to return to Alaska.