We have not been to Whittier, but have taken several cruises with Kenai Fjords in Seward. I have not made resevations in the past, just stopped in when we got there, but I have not been there since 2008. Trips have been enjoyable. We also had a cruise on Major Marine and the weather shortened the trip. They gave us a partial refund since we did not get the full trip.
If you get to Valdez, I highly recommend Stan Stephens Cruises. They serve a lunch and afternoon snack on the longest cruise. Again I usually book after we get to town or call a day or two ahead once I know a weather forecast.