My recommendation would be to fly into Anchorage, stay downtown, take the downtown trolley tour, get a nice meal at one of the Breweries, then take the train in the morning to Seward and spend a second night there. You can take a Kenai Fjords tour when you arrive in Seward, and go to the Sea Life center the next morning before boarding the ship.
Once you get to Vancouver, plan on staying there for a night or two and then taking the train to Seattle and flying out of SeaTak. Both Vancouver and Seattle are really great cities and worth spending some time there, so you can figure out if you want to spend time in Seattle also.