I would echo what FTI said. We just got back from our honeymoon and took that train. We had 2 days (1 night) in Seward, took the train to and from Girdwood. The train route is scenic, but the road route is also very pretty.
On the train we saw 3 black bears and 2 moose. But all of them were hard to take pictures of as the train was moving fairly quickly. However the route still takes longer than taking a car with multiple stops. If you do take the train, the upgrade to goldstar is more than worth it.
The Wildlife cruise we went on in Seward was exceptional! I recommend staying at least one night if doing the bay cruise, as train-cruise-train is a very tight schedule.