I stayed at Friday harbour House when I was visiting the islands. It was amazing. The room was great, with a fire and great view (even though it was only partial sea view). the free coffee and snacks were lovely and home made. We sat out the front and watched the ferries come in . Really relaxing.
It might be a bit expensive but worth it.
When we visted Orca Isalnd we stayed at the Deer Harbour resort. A bit more isolated - but again stunning. We had a cottage with a hot tub out front and again amazing views.
The islands are fantastic. have a great trip.