When we lived in Skagway 1996-2002 we traveled to Juneau frequently 6 to 8 hours by ferry (Alaska Marine Highway) or 1 hour by air (Skagway Air Service).
A couple of points to consider.
At least in those days the ferry did not operate everyday and the schedule worked around the clock. What that meant was that sometimes the ferry departed at 2:00AM sometimes at 10:00AM and sometimes in the mid afternoon. It could be at anytime of day or night. The ferry terminal in Juneau is as I recall is about 3 miles from Juneau. If we had shopping to do we would put the suburban on the ferry and then load it to the gills for the return to Skagway.
The air service only operates in daylight (VFR rules). In the summer the days are very long however. Skagway Air flew Piper Cherokee 6s (single engine low wing 6 passenger planes). I always sat beside the pilot up front because it provided a great view and gave me the feeling that if the pilot suddenly died or became incapacitated I could fly and land the airplane. We used it frequently when we flew outside (the term for anything outside of Alaska). There were occasional weather delays and turnarounds. Once we flew almost all the way to Juneau and had to turn back to Skagway after getting to within 3 miles of the Juneau airport because of it being socked in. On a positive note we could drive our suburban right up to the airplane to load our bags and then park just off the runway while we were gone (pre 9/11 of course). The Lynn Canal and the Juneau ice field are spectacular from 3,000 feet.
Life in Alaska is an adventure. For most folks Alaska is a trip of a lifetime and they make the mistake of waiting a lifetime to go.
Go when you can and expect an adventure.
John Bush