"We are looking at the train from Anchorage to Seward, pros/cons?"
The train is scenic and it gets you there. Using a one-way rental car would be expensive, but allow you to stop and sightsee along the way.
If you fly into Anchorage and the day before and take the early morning train offered by the Alaska Railroad, you'd have time for a Kenai Fjords cruise before boarding your ship.
Here's the local vendors at Icy Strait Point (Hoonah): http://visithoonah.com/experiences/ Another option for halibut fishing is to fly into Anchorage a couple of days before your cruise and fish out of Whittier or Seward.