One of the highlights of my trip for years ago was the White Pass train excursion. Loved it, but probably will do something different this trip. I recommend you book it through your ship cuz it sells out.
WE too did that excursion and loved it, although its a bit on the long side, 3-1/2 hours..The scenery is just breathtaking, something you just got to see. They allow you to go outside the train car on back and stand, which I did most of the trip. I must admit, on the way back down, I sat down and fell asleep, guess quite a few people did the same, but is really is something to see. Its very well narriated with lots of interesting information.
Have done Alaska 5 times (#6 in July) I love Skagway and my favorite excursion of all there is the White Pass / Yukon trip, where you are taken out into the Yukon via bus (the scenery there is spectacular) and come back into Skagway on the White Pass. It still gave us time to do some strolling around Skagway. It is fantastic!
Yes there are bus / train combo trips. BUT be certain to choose what is your preference. There are shorter ones that just return to Skagway from the summit - (in BC). Longer bus rides take you into the Yukon.
If you love antique trains and mountain vistas, then the train trip is "must see". I too recommend booking through the cruiseline. The cost is about $100 and can be reserved 60 days prior to sailing. That's what I did last year. My tour also included a visit to Liersville trail camp which is an amusing living history presentation of the gold rush days.