I just got back from the June 7th sailing. Really, layering is the key because you never know what it is going to be like...and a strong wind can make an otherwise comfortable day seem much colder! I'll tell you what I wore, and it should give you an idea of what to pack.
For all three ports and while outside on Tracy Arm day, I wore a base layer shirt...this is the exact one I had and loved it (
http://www.rei.com/product/795083/rei-lightweight-polartec-power-dry-long-sleeve-v-neck-womens), a short sleeved t-shirt over it, a lightweight fleece jacket, and a waterproof/wind proof/breathable jacket (this is the one I had...but I was lucky to get it on sale (
http://www.rei.com/product/794277/rei-kimtah-jacket-with-event-fabric-womens). On bottom, I wore this base layer (
http://www.rei.com/product/795095/rei-lightweight-polartec-power-dry-long-underwear-bottoms-womens) and water resistant/windproof pants over it. The only hat I used was the hood of my jacket, and I brought gloves but only used them a couple of times because they made it difficult to use my camera.
For Tracy Arm, Skagway, and Juneau I only took off layers while inside (inside the train in Skagway and inside the whale watching boat in Juneau). While outside in those ports I was glad I had all of the layers. In Ketchikan, I was comfortable but would have been fine with less layers...it was not as cold there. Now, I should mention that I am from Texas, so I am probably more sensitive to the cold than most! I saw just about everything when it came to people's clothing on the boat. There were people that were much more bundled up than I was, and there were also people walking around on deck in short sleeved shirts. I really think it depends on your personal tolerance for cold weather.
As far as on the ship, I had read so many reports that it was cold in the dining rooms and common areas, however I was actually hot most of the time while inside and wore short sleeves to dinner and the shows each night, and never needed the cardigan I brought. My kids burned up in the kids club...they ended up wearing shorts and t-shirts while there. I had packed one pair of shorts for each of us, but my husband and I never wore ours.
I brought jeans, but only wore them on the ship...I did not want to wear them in port because you never knew when it might start raining, and I hate wet jeans. The water resistant pants I had were very comfortable (I bought them at REI).
I'd say the best item I brought was the windproof/water proof jacket. I think it is worth it to invest in a high quality windproof/waterproof jacket that is still breathable. We were VERY lucky to not have much rain on our cruise, but it did sprinkle on us a few times, so I was glad I had the water proof jacket.