For Juneau I highly recommend visiting the Mendenhall glacier. There are busses at the dock that will take you there and return you. Not sure the the going rate these days but it's pretty reasonable.
If the weather's clear take the Mt Roberts Tram. You can also catch this right at the dock. No need to pre-book this and only go if the weather's clear.
We really enjoyed our whale watch trip as well. You'll likely see whales from the ship but not very close. The whale trips do get close.
For Skagway....never did the drive so can't compare but the White Pass train trip is spectacular.