Well, I wrote a long,excellent (if I do say so) reply but the site froze and I lost it. So, the Cliff Notes version -
Ask an Alaska-specialist travel agent about small-ship cruises to Alaska. They are pricey but they are worth it. That's how we cruised Alaska (can't afford to do it twice) and it was fantastic! Got up close to wildlife (in a safe way) and we were able to check out the scenery in a more relaxed (and casual) manner. Haven't yet tried the ferry, but there are some advantages to that mode of cruising as well.
Yes, you can take the Alaska RR to Denali, though you will need to find a hotel there that offers a shuttle to/from the train. You can also rent a car & drive it. Not a problem.
Best time of year: May through the first half of September. We did our Denali trip the week after Labor Day (years ago) and the fall colors were stupendous! Nice pleasant weather, in the 50s. We took our cruise in early to mid-May, and the only thing we missed was orca - too early for them. Saw plenty of humpbacks, though.
Ditto msmith on the balcony cabin. If you do not do the small ship or the ferry, BY ALL MEANS get a balcony cabin. Yes, it will be windy and chilly - dress for it, in layers, and enjoy.