I've never been that far north, but I've got family in Ketchikan, I've been there several times.
I've never been on a whale watching tour, but every time we've been out fishing, either guided, or in my brother's boat, we've seen a whale or two. I'd suspect, if you're trying to see whales, you shouldn't have any trouble finding them. There's eagles everywhere too, seeing bald eagles up there, are like seeing crows down here.
Porpoises, seals, sea lions, whales, all pretty common. I lost a real nice halibut to an shiny happy person sea lion when we were up there about a month ago, stole my fish and 300' of line trying to fight to get the fish back. Fishing about 600 yards south of West Rock, which happens to be a sea lion rookery. Sea lions stink, like really stink, pungent, just FYI.
Fishing and cabbing are some of my favorite things to do up there. You've not had crab until you've had it straight from the ocean.
Freshwater fishing is fun up there too. Trout, salmon, steelhead, etc. You'll be too late for salmon runs, but trout fishing should be good.
Hiking, fishing, boating, are what I like to do.
Ketchikan has A LOT of touristy stuff too, it's usually your first or last stop on an Alaskan cruise. I don't know if any of the cruises actually go to Anchorage? I think most stop at Seward or Whittier on the north end. If they do go to Anchorage, there'll be plenty to keep you occupied, all of those towns really cater to the cruises. Though, the cruise season normally ends sometime in September, so depending on how late you're going, most of the seasonal hospitality folks may have gone home already.
I once took a boat and fly tour out to Misty Fjords, it was gorgeous, and I'm glad I did it. However, with the number of tour planes that have gone down in the past 4-5 years, I'm hesitant to do it again. The very plane we were on, on that trip, De Havilland Otter, crashed into a mountain, killing everyone onboard, exactly 2 weeks after we flew on it. Different pilot, but same plane, tragic, and a little unnerving.
I don't have any Anchorage specific info, but I'd be happy to answer any questions I can.