It really depends on what you like to do. Our favorite thing was a flight seeing adventure on a float plane out of Ketchikan, booked through a local agency we found when we got there. It was so much cheaper than going through the cruise line.
As for clothing, plan on layers and waterproof jackets. If you don't like the weather in Alaska, wait 15 mins and it will change. Unless you're planning to hike on a glacier, you won't need special shoes.