Cooper Yachts and Desolation Sound Charters are the two main options for bareboat charter near Desolation Sound. Desolation SC have their HQ at Comox, across the water on Vancouver Island, whereas Cooper are at Powell River on the same side of the Straits of Georgia. In terms of relative location there is not much to choose between the two. However the Cooper facility at Powell River is an outstation from their main base, at least a days sail away, at Granville Island in Vancouver - so I suspect that local support from Desolation SC might be stronger. Desolation SC also have been doing charters in this immediate area for much longer. Both companies are very well established and have good reputations.
I have chartered twice from Desolation SC and their pre-departure chart briefing was excellent. You can fly via scheduled flights into to both Comox and Powell River.
Desolation Sound is simply magnificent. Anchoring is sometimes a little challenging because the water often gets deep quite quickly near the shore. Be prepared to put a stern line ashore in many locations. Enjoy!