For general information. Amtrak, is far superior to Quick Shuttle for a Seattle/Vancouver transfer, IF you have an extra day.
As for Whittier, there is inaccurate information above. They certainly do have lodging, and I would NOT recommend you "take the Princess transfer". A poor idea, with your listing of a Prince William Sound boat tour.
The better PWS boat tours leave at 11am and sail Esther Passage. The others leave at 1pm. With you going so late in the season, see if you can purchase a used, cheap Toursaver or Northern Lights coupon book for a 2 for 1 coupon. You do need to VERIFY, if space is available now. From either of these you would take the Alaska RR back to Anchorage. There is no reason, to do this "through Princess". Arrange this yourself.
I would then get a rental car, and decide what you want to do. Considerations- Hatcher Pass and Independence Mine/hiking, Talkeetna with McKinley flightseeing, Matanuska glacier trekking- look for the longest tour available- time flys by. Or, if of interest tour Anchorage.
Most important- FIND OUT, what may be available to you, then make your choices. Allow a 2 hour window at Anchorage airport, it's slow moving and can be congested.