We did that cruise last year. The best part of our trip was in ketchican. We took a float plane trip from seawind aviation. The family that runs this was great. The views from the plane were awsome. Our ship was a little late docking. The waited for us. After, the offered us one of there vans to tour the island. On the flight, we landed on a small island in a lake in the mountains.
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In juneau we chartered a boat thru ak-whale whale watching. The smaller boat was the way to go. The bigger boats were 65 per person to be shoved in with 100.00 other people. The private boat was 105.00 per person. The paired us up with another couple. 4 people plus the 2 crew on a 33 foot boat. We got much closer than the big boats could.
With both of these, we had time to wonder around the towns. Took the cable car up to the top of the mountain.