The season runs from May until September, if you go earlier or later you risk not seeing much of the wildlife such as Bears and Salmon. Most cruises will have a day or two of bad weather, that is the nature of the region, and the ships are all so delightful and cozy that you can still have awesome days, much like enjoying an alpine chalet when it's snowing outside.
 
That being said crew who work this have advised me that you should try and book either two 7 day cruises back to back, or a 14 day one to allow for missing out on some things when the weather shuts down.
 
One such most do excursion is a helicopter flight to the top of the mountain to go dog sledding. It is very expensive at about $700 per person, but it is an experience beyond your wildest imagination.