I do not recommend the cruiseline rail transfer. First off, it is $40 more than the regular run. You also have no time for much touring beforehand in Anchorage and little in Seward. Far superior is to take the regular run of the Alaska RR and getting into Seward a little after 11am. Then spend the day with some spectacular touring options. My top choice is a Kenai Fjords boat tour, way superior to anything you will see from your ship and if wildlife is a priority, this is your only opportunity for varied wildlife. www.kenaifjords.com
has an 11:30am tour, they pick up at the depot, store your bags and shuttle you to your ship.
Other Seward options are Seavey's Sled dogs, Godwin's glacier helicopter, Exit Glacier, Sealife Center. Take advantage of being there. Here are some photos of Kenai Fjords- http://community.webshots.com/user/budgetqueen
As for shore tours- way too many excellent choices. Look over a shore excursion list and narrow down your interests. This isn't the place to skimp either.
It is not always cheaper to book independent, but they will give you a better tour with much more personal attention, longer tours etc. I recommend having all plans and reservations in place before you leave. You need to determine what tours you are interested in, then find a vender.