I totally agree with
@Dug720. CC has a lot of good information (if you can ignore some of the crankier folks over there). I especially like their destination specific boards. Lots of good stuff, and not as much snark as you see on their individual cruise line pages.
I will offer a little advice, based on our experiences there (2 cruises and 1 land based trip).
Weather - it's so unpredictable. It "should" be warmer later in the summer than in May and June. Doesn't mean it will be, though. For Alaska, just pack layers and good rain gear and hope for the best.
Itinerary - You'll have to decide if you want a round trip or one-way. Having done both, we greatly prefer the one-way as it allows you to spend additional time in Alaska either before of after your cruise. Not everyone has the time and/or budget to do that, though. You also will be booking travel to and from from different cities, though that's never been that big of a deal to me. You will hear a lot about Glacier Bay which Disney doesn't do. It's amazing, it really is and I'm glad we finally got to see it on our 3rd trip to Alaska. But we had incredible trips prior to that as well, without Glacier Bay. We loved Tracy Arm and Hubbard Glacier is just incredible, an amazing expanse of ice. Hopefully Disney will continue to offer Hubbard from time time as they did this summer.
Excursions - Skagway has the train and tons of people do that and love it. We never have because for some reason it's just never appealed to us. We booked a private guide that took us up to Emerald Lake and Carcross in the Yukon and it was fabulous (Skagway Private Tours). We did the Takshanuk Mountain Trail 4 X 4 through Disney on our first cruise and that was a lot fun - our son especially loved that (he was 14 at the time).
Juneau - A lot of the excursions here involve Mendenhall Glacier and whale watching. Both are terrific. There is also a tram you can ride that goes up to the top of a mountain, but we've never done that. We used Rum Runners for their 6 hour photo and fishing safari and had the most amazing day - and now have a freezer full of yummy salmon! On the Wonder cruise we did the Alaska Whales and Science Adventure. It's a nice alternative to the large boat tours as it's a much smaller group and the guide did a great job of engaging the kids in activities.
Ketchikan - There are a lot of different things to do in Ketchikan. You'll just have to read some trip reports and such. We went bear watching both times. We used Island Wings to Anan Creek (amazing, I can't even tell you how many bears we saw! - book early as the park service only allows 60 people per day at Anan) and Neet's Bay by Floatplane through Disney (also terrific, though Anan had a lot more bears) If you are interested in bear watching, be aware that most tours begin in late July and go on through August when the salmon are running. I'm not saying you won't see bears in May / June (it's certainly possible), but a lot of the bear tours won't be offered then. There a lots of other (less expensive) things to do in Ketchikan besides bear watching. It's just a particular interest of ours, so we've made room in our budget for it both times we've been there.
Excursions in Alaska can be expensive, though they do vary widely. There are plenty of economical things you can do, but you can also drop a ton of $$$$ here. Just do your research.
Vancouver is a great city and we spent 3 nights there prior to the cruise. I'd highly recommend at least a night or two - so much to do! We loved Stanley Park, Gastown, Flyover Canada and especially Granville Island. We also spent a lot of time just hanging out the waterfront watching the float planes and checking out the cruise ships. We considered going to Capilano suspension bridge, but simply ran out of time - something to save for next time! We sailed out of Seattle on the Wonder and it's a fun city as well.
There really isn't a "best" way to see Alaska - and I say this having been there three times now. You are going to read a lot of stuff and people have strong opinions, but take it all with a grain of salt, including my advice. Alaska is beautiful and it's enormous. There is so much to see and do, that unless you just move up there for a summer you aren't going to see it all anyway. Read up on it, pick a trip and then just sit back and enjoy it.