I've done two whale watches. One over thirty years ago out of Boston (mid-June), and one two years ago out of Juneau (first few days of June). As someone earlier posted, one major difference is that it takes an eternity to get to the viewing area from Boston, but does not take take long at all from Juneau.
Anecdotally, the Boston watch had far more whales. We were able to just sort of drift and see breaches, flukes, and even one swimming under the boat. In Juneau the different tours' boats were in communication and would converge on locations as whales were sighted. We saw four total (all humpbacks), but two were a mother and calf so that was cool.
Despite what I felt were lackluster results, the Juneau watch was still worth it. If nothing else we had a nice outing on Auke Bay with an informative guide, though I will say that we had fantastic weather that helps it be remembered more positively.
