Late June is a great time to go, with the longest days of the year. You'll be able to read a newspaper out on deck at 11pm with no problem.
Most ships hit the most important ports of Juneau, Skagway, Ketchikan and a ride through Glacier Bay or similar. Some ships are still going to Sitka, a port with lots of history and wonderful things to see. To me, Skagway is the absolute "don't miss" in Alaska.