The Stan Stephens company runs a first class tour. Although it seems a little pricey (it runs around $130/person to go on the Columbia/Meares Glacier Tour that we went on), we felt like we got our money's worth and more. The boat itself is a large catamaran—we went on the Spirit of Valdez, which was just built in 2004, so it's a brand new boat. The captain is multi-talented—he manages to give a narrated tour while steering around ice chunks and pointing out wildlife—we were truly amazed by that. You begin in the small boat harbor in downtown Valdez, and then you're taken out to the Prince William Sound.
On this tour, you see 2 glaciers—the Columbia and the Meares, and it runs about 9.5 hours. However, while we were there, our tour ran about 10.5 because we kept seeing so many animals. As you travel towards the glaciers, the staff will point out animals along the way, and normally the captain will stop and try to get closer. We saw quite a few animals, including 4 black bears, bald eagles, sea otters, sea lions, mountain goats, and dall porpoises. This cruise comes with lunch and a snack—at lunch, you get chicken alfredo on rice with a breadstick and cookies. At around dinner time, they feed you a snack of clam chowder and crackers.
Throughout the trip, they serve complimentary coffee, tea, lemonade, and hot water. I highly recommend bringing packets of hot chocolate or cider if you aren't a coffee/tea drinker—they charge 50¢ for each packet of hot chocolate, cider, etc. In addition, you can bring snacks along with you, or they do have a few for sale along the way. At least in early June, it was still pretty cold out near the glaciers. It's a good idea to wear lots of layers and bring along a warm coat, hat, and gloves.