I strongly recommend a balcony cabin for Alaska, or at the very least, an outside cabin with a big window! The scenery is nonstop, and days are very long (if you are sailing in late June, there probably will not be any complete darkness outside at all). I'd hate to miss a minute of it! Other than right up near the bow, I don't think there's a bad spot, as there is little rough water on Inside Passage cruises. One-way cruises between Seward and Vancouver/Seattle will give you a little more opportunity to bounce around.
Do you have a cruise-oriented travel agent in your area? If so, I'd advise seeing them about this - there are so many choices between cruise lines, ships, and itineraries, each with subtle - or not so subtle - differences.
However you go, enjoy it! Alaska is fantastic!