I take it that you are taking the cross gulf ferry to Juneau and changing ships there, for the run down to Bellingham. We have done the Skagway to Bellingham, run in the past and enjoyed the trip greatly. But have never done the cross gulf leg before. Believe the cross gulf runs very seldom, perhaps once or twice a month.
As far as I know, the service dog should be able to be with you in your cabin and around the ship under the ADA rules. Hotels can't keep a service dog out, so I would guess the AMHS ferry boats would be the same.
Have you given any thoughts of driving over to Haines or Skagway to get on the ferry. The cross gulf ferry stays way out in the water, a long ways from shore. Not much to see out there but water and the Gulf of Alaska is known to get very rough at times. Not unsafe with the large ferry, just uncomfortable.
