October is cooler, but there are some killer deals I've seen on Dargal.com for interliners during that time. Mainly repositioning cruises from Alaska back down the West Coast. There's not going to be a whole lot of difference weather wise between September and October in Southeast Alaska. Typically anytime August or later is pretty much the rainy season. If possible, May is the best time to go. Before school lets out and the flight loads are low, and the weather is usually a lot nicer. Good luck.