This is going to be tricky.
I've glanced at the Alaska Rail Road, and couldn't find a direct from Seward to Whittier. I'm guessing that you'll have to take a train from Seward to Anchorage then one from Anchorage to Whittier (or have the cruise line take you from Anchorage to Whittier).
Another option is to rent a car, it's a lovely drive and there is a car rental return in Whittier.
