Being that you want "trip of a lifetime" tours, NEVER wait and book at the dock. Always, have all reservations and plans in place before you leave. Your "dock" selection will be extremely limited with most tours NOT available, along with inconvenient times.
As for best tours, best will be what is best for you.
I too always am on flights, and actually between a whale watch and glacier helicopter landing, the price difference may only be about $100.
Some of my top tour choices in your ports- glacier helicopter landing, Misty Fjords float plane, Sitka, wildlife boat tour.
I book all independent, and never cruiseline tours.