I have rented cars in all ports and I always see something new.

If not considering the White Pass RR, a car in Skagway is ideal- go to Emerald Lake 75miles north and return- little scenery past that point. Juneau rental is good if you are in port all day and want to see several attractions- fish hatchery, Mendenhall Glacier , Glacier Gardens, Auke Bay, St. Thersa's Shrine, Chapel on the Lake etc, do your laundry.

Rent from either All Star or Rent a Wreck- these are the only 2 companies that provide dock pick up. Ketchikan- I have gone to my "bear watching spot" and hiked out at Ward Lake, you don't need a car in either downtown area of Skagway or Juneau.