Since it's your honeymoon, please do yourselves a favor and consult with a cruise-oriented travel agent about this. There are so many good options to choose from, and so many details to think about when it comes to a wedding - why add to the stress by trying to figure out all the details of your honeymoon?
As far as your timing goes, third week of May is usually a pretty good time to go; fares are a bit lower than they will be later in the summer, days are long, bugs aren't quite out in force yet, and the humpback whales are back. Orcas may be also (we missed them, going the first and second weeks of May). Weather will be cool, so dress in layers, and be sure to take rain gear (that's true any time of year in southeast Alaska). And make sure to book a balcony cabin!! Scenery is nonstop, 24/7.