We took a group of 12 to Pybus last August. Lodge was great, and flexible with what everyone wanted to do. Highly recommend Jeff Davis (boat captain) - and you should request his boat in advance. The lodge likes to grab smaller halibut first on fishing days, then progress to other species. Lodge - A. Fishing - B (plenty of restrictions in the area around Juneau). Menu - B. Scenery and overall wildlife - A+++. Feel free to DM me if you want any details. They are pricey, but most of the lodges in the area are.
FYI, I would not rule out taking the ferry from Juneau to Sitka and fishing from there either. I think they still have the high-speed ferry running.
EDIT - if Pybus has a spot, and you go there, I would encourage your wife to go fishing...even if she doesn't fish. The scenery, whales feeding, orcas, and other wildlife are well worth the boat ride each day - as is the trip out to see the glacier.... you fish in both directions.
We did come home with about 80 lbs of filets.