We were in Alaska last year in June.
In Skagway, we did the White Pass & Yukon rail trip and enjoyed the experience and the scenery.
In Juneau we booked a half-day whale watching trip with Orca Enterprises in the morning. Our shuttle driver dropped us off near Mendenhall Glacier and we walked over there to see this magnificient glacier and then took the blue-bird bus back into town. We skipped the tram since the skies were overcast and the clouds were low enough to preclude us from seeing much from the top.
In Ketchikan, we walked up to the Totem Heritage Center and the salmon hatchery. Walked back into town via Married Man's Trail. That afternoon we had a spectacular excursion to Misty Fjords -- went out by catamaran and saw seals and orcas, and returned by floatplane.