In my experience (six SE AK summers so far) Prince Rupert is a great choice for a launch. If you pay attention to wind vs tide, and go when the conditions are reasonable, the Dixon is not that tough at all. PR also has indoor storage for truck and trailer, and the road to PR from the lower 48 is no problem at all. There's so much great cruising between PR and Elfin Cove it's hard to describe adequately.
If you're going to try launching at Skagway, you need a healthy respect for Lynn Canal, some 80 miles of straight channel that very often funnels the wind, creating pretty rough conditions for a small boat. And there are few safe harbors to duck into. A fast boat like a TomCat has a better chance to zip through there safely.
As for a week for that tour out of Juneau, I'd agree that that's awfully short for a small boat, given the weather possibilities. I've picked up guests in Juneau and Sitka many times, and would not agree to much less than two weeks unless the guest was willing to miss a plane.
Here's some info on Glacier Bay and permits:
Glacier Bay
For many cruisers a visit to Glacier Bay is a lifetime goal. Sitting right in front of a tidewater glacier in your own little boat, watching 100 or 200-foot chunks of ice calving into the sea, is an experience never to be forgotten. And the critter-watching is excellent. Visiting Glacier Bay is no trivial undertaking. It is a very big place, and with its huge snow-covered mountains has some of the most challenging weather in Southeast. Distances are great, anchorages are few, and there are several restrictions.
Only 25 boats are allowed in Glacier Bay at a time, and you need an entry permit. Many cruisers make reservations ahead of time, and then find that weather or other difficulties make their schedule unworkable. From our experience, the best way to get a permit may be waiting to call Park HQ at Bartlett Cove until you’re close by (say at Hoonah or in Icy Strait), and the forecast for the next few days looks reasonable. For best odds, call right at 6:00 AM (they’re open 6 AM - 10:30 PM) on either VHF 12 or (907) 697-2627. Chances are fairly good that a cancellation has freed up an entry permit, and you can take advantage of it if you’re nearby and ready. If no permit is available, try again later or the next day – they don’t mind you asking again.
You’ll need a minimum of two days in Glacier Bay to make it to and from the Margerie Glacier. The Margerie, at the top of Glacier Bay some 60 miles from the entrance, is a spectacular and active calving glacier. You can get fairly close to its face, some 200-300 feet high. On the way north, the Lamplugh and Johns Hopkins glaciers are spectacular as well. With a third or fourth day, you could see quite a bit more, at a less frantic pace, and have better odds of dealing with uncooperative weather.
To start your Glacier Bay excursion, you stop in at Park HQ and attend an orientation on do’s and don’ts. As of 2008 the lecture was given only at pre-scheduled times, so you’ll want to plan your first day accordingly. You might try entering the park very early, calling Bartlett Cove to check in when you cross the boundary. Tie up at the float, and catch the 8 AM orientation (bring your National Geographic map of the Bay so you can see details). With good weather, you should be able to make it a good part of the way north, to an anchorage at North Sandy Cove, Blue Mouse Cove, or in front of the glacier in Reid Inlet.
Parts of the bay are considered whale waters, where boat speed is limited to 13 knots. Even with a fast boat, you’ll find that first day pretty full, getting through the entry process and on to an anchorage, unless you anchor right there in Bartlett Cove (the float’s limited to a three-hour stay, except for dinghies). If you anchor, be aware that Bartlett Cove is open to the west, and can get pretty lumpy in a west wind. You could also anchor fairly close at Fingers Bay (enter carefully).
From North Sandy, Blue Mouse, or Reid, you could head north the next morning, spend 2-4 hours at the Margerie Glacier, and come back south to anchor again. As you slowly approach the glacier through fields of bergy bits, keep a sharp lookout for small ones called “growlers”, only a foot or a few feet long, and often nearly clear. These weigh more than you might guess, and can give your boat or your prop quite a thump. The smaller ones make great ice for the cooler.
If you get back to Bartlett Cove for your last evening, and are out of permit days, the following morning you can call and obtain a “transit permit” to leave the park that day.
If the weather sounds intimidating, or you’re able to get only one or two permit days, a nice way to see Glacier Bay is the Fairweather Express tour boat, operated by the park lodge. For about $180 per person (2008), you can have a wonderful day tour, seeing some of the finest glaciers and lots of wildlife, with a friendly crew and on-board naturalist. For us, one ticket cost about the same as touring the bay in our own boat.
Even with only a single day’s permit, you could still enter Glacier Bay, get your orientation, and then anchor in Bartlett Cove. The next day, leaving your boat at anchor, row your dinghy in to the float (motor vessels may not be operated without a permit for that day) and catch the tour boat. On the third day, call for a transit permit when you’re ready to go, and exit the park.
If Glacier Bay doesn’t work out for your cruise, the Tracy Arm, south of Juneau on the east side of Stephens Passage, is a fine alternative. In fact, you might give it a tour even if you’ve already been to Glacier Bay. It’s a particularly beautiful steep-sided fjord, with two tidewater glaciers, lots of icebergs, far less challenging conditions, and few of the complications of Glacier Bay.
