I also cruised in mid-September. We had great weather and it was fairly warm. Upper 50's and low 60's. The only day we had rain was in Juneau and I was happy I had a rain suit for our whale watching excursion.
Predicting the weather is something that not even the professionals do too well so it's hard to say what the weather will be like five months from now but September is a rainy period but it doesn't mean that it will rain all the time.