I'm not a fisherman, but from what I understand the fishing is significantly better our of Ketchican that Juneau.
Everyone we saw coming back from fishing in Ketchican has salmon. Most in Juneau got shut out.
We just got back from the June 22 Celebrity-Mercury Vancouver to Seward cruise. We booked a whale watching trip from an independant at the dock at a significant savings over the cruise line. We ended up with four other Mercury passengers on a Bayliner cabin-cruiser. It was great being on a small boat and getting away from the crowds.
On the way back (from Auke Bay), we rode on a mini-bus with some other Mercury passengers that were returning from a fishing trip. They caught their limit of salmon and seemed quite happy with the whole thing.
My husband did a flyout fly fishing trip in Juneau through HAL cruiseline with Bear Creek Outfitters (1-907-789-3914). He is not a fisherman and had never been fly fishing but loved it. We were there in mid July. He caught a dozen salmon and said the flight and the fishing spot was beautiful. Everywhere he looked he saw a scenery worth being on a postcard. Pricey at $325, but it was one of his favorite adventures. Good Luck!!