We are big fans of independent whale watching companies. In Juneau, we like Jayleen's Alaska and in Icy Strait Point, we like Glacier Wind Charters. Both companies are great vendors and have lots of great reviews on Cruise Critic as well as TripAdvisor.
Since independent vendors have a tendency to book up fast, we always book ASAP as we don't want to miss out. With that being said, do what you feel most comfortable doing for your cruise.