Ah the 64 K$ ? as they used to say.
Inside one weekers return are more frequent from Vancouver so there's my first suggestion. Although there are some from Seattle and the air is cheaper usually to there they sometime miss out on a lot of the "Inside" cruising because of time constraints.
Cruise lines is a real personal thing. Pretty well all main line major cruise lines have ships up here so you takes' your pick.
HAL, Celebrity, Princess & RCL in no particular order would be a good choice. (There are others) If you have never cruised before it really won't make much of a difference I don't think. Then you go on another line and you have something to compare. All ships do not go to all ports so if there is something you really want to do say the WhitePass and Yukon RR you have to make sure your ship goes there (Skagway)
Time to go: Early and late could be cheaper. July AUG of course more kids. My TA advised there are basically no rooms available for the rest of this month and September to Alaska and they do a lot of business.
Weather. It's the coast and hit and miss all the time. More animals moving around in Spring time. Whales take a while to get up there. So early would limit that on the other hand. Getting into the face of the glaciers is sometimes iffy and more so early season. Less fog early more later.
So best time.?? When your time, budget and itinerary all come together.