As has been said, it all depends on what you want to do when you decide whether to cruise or fly-drive.

For our trip, we flew into Anchorage, then rented a car and went to the Kenai peninsula, did some kayaking in homer, then did some hiking (the harding icefield trail is pretty awesome, i'd say, although somewhat of a strenuous day) and went for a glacier cruise (saw whales, bears, birds, dolphins) from Seward (which is where all the cruise ships go), then drove up to Fairbanks, hung out around there for a few days, then went camping in Denali before heading back to Anchorage, hanging out for the sunset in Anchorage over the water before heading to the airport to find out that we'd missed our flight by 24 hours (but that's another story)...

I'd definitely recommend seeing some of the interior of Alaska. Up around Fairbanks is pretty cool, and Denali national park is worth the trip, I'd say -- don't take the "wilderness tour" bus, though -- just take any shuttle bus and you'll see more wildlife than you've ever seen before... (unless you've been to Africa, i guess...)

We also camped most of the time we were there, which made the whole long-daylight thing a major issue (although we were there in August, so the days weren't as long as they are in June). Mostly we went to bed later than usual (around sunset, which was at 10-11 pm), then woke up late-ish to find that we were the last ones in the campground. It's great to have 18 hours of daylight to play in, though..

Dan