Hi Andrea!
We're getting ready for our 3rd September cruise. There's no way to predict Alaskan weather. The first time we went, it was beautiful in-land from Anchorage to Denali and rain showers in Seward. College Fjord was beautiful and Glacier Bay was cloudy and gray. It was rainy at all the inside passage towns (Juneau, Skagway, and Ketchikan).
Last September it was rainy in Anchorage, but cleared quickly. Seward and the Kenai peninsula were sunny and warm - just cold around Exit Glacier and wind-breaker weather in the town of Kenai. The inside passage was beautiful. We only had rain in Juneau! Specifically, it was sunny in College Fjord, Glacier Bay, Skagway, and Ketchikan!! The only coat weather was near the glaciers in Glacier Bay.
All you can do is be totally prepared for everything!
Shar