Juneau is your best bet for food. Tracy's Crab Shack is along the main dock. They have king crab legs (though if available, they are extremely expensive). They also have a tasty crab bisque. It is convenient and very popular. My favorite place is actually a food truck called Deckhand Dave's. It is very close to the dock, about a 5-7 min walk. They sometimes have chowder but it is ALL about the fish and chips. They have 3 kinds of fish, typically rockfish, salmon and halibut. You can mix and match or get 1 kind. The fries are amaaaaaazing as well, as is the homemade tartar sauce. They also serve excellent fish tacos, too. Though it is a food truck, there are tons of tables (some covered by a tent in case of rain). There's also an oyster and champagne bar, an old boat converted into a bar with Alaskan beer on tap, and a crepe place as well. I love Deckhand Dave's so much, I'm planning to eat there twice when I visit in July. (Our port time is 11am to 10pm or something similar).
I haven't found anywhere amazing in Ketchikan recently. There was a place 10 years ago with amazing fish and chips but they closed, sadly. Next time, I'm planning to try Ketchikan Crab and Grille. Ketchikan is a fantastic place to buy salmon, however. Both canned and smoked are everywhere.
Haven't been to Icy Strait Point yet, though the restaurants near the dock have poor reviews. The Fisherman's Daughter looks promising but you'd have to make the 1 mile walk into Hoonah to get there, unless you had an excursion in town. I'm planning on doing whale watching when I visit next month, so I won't have time but I'd love to hear if anyone else who went thought it was worth the effort.