We've met many Canadians who launch in Skagway and travel down Lynn Canal to Icy Strait, basing out of Hoonah to fish for a week or two and head back. Jay of Hunkydory on the c-brats site has cruised northern SE AK launching in Skagway more than once.
We've always come up from the south, launching in Prince Rupert 11 summers so far, though we did come all the way up from Everett WA one year. We find crossing the Dixon Entrance a good way to go. And the drive through BC to PR is a pleasure as well.
Whether you do Lynn Canal from the north or Dixon Entrance from the south, the key is to understand the current weather conditions and forecast, and be especially wary of wind opposed to tidal current. Have bailout anchorages identified ahead of time, so that you can duck in somewhere if it gets unpleasant.
Lynn Canal can be a wind tunnel with nasty conditions. Listening to conditions reported on the VHF weather, the northern half of Lynn Canal often has considerably stronger winds than many other places in SE AK. And there aren't many anchorages along the way. One time we did cruise up to Haines and Skagway, we got stuck in Haines for 3-4 days waiting for Lynn to calm down enough for a do-able but still rather unpleasant slog back down to Juneau. 20 knots or more in any of the long straight channels in SE AK can build a pretty bumpy chop, but Lynn is a little more susceptible as its sides are tall and it funnels the wind.
Waiting until the situation is right to cross the Dixon can sometimes take a day or three, but when it sounds like it's all coming together we leave early and go, and it is usually mostly a very pleasant trip. Heading back south in late August I've had to wait several days 2-3 times, but again when conditions are right it's a lovely trip. I'd look for winds not forecasted to exceed 15 knots, or 20 at the most, and wave heights 1 meter or less at the Central Dixon Entrance buoy. One of the worst combinations (to avoid) is wind from the west and a strong ebbing tide just as you're crossing the most open part of the Dixon.
We travel mostly at only 6 knots, so we're out there for quite a while, during which the combination of wind and current can change several times, which does make planning more complicated. Even at 6-7 knots, you can make it from PR to Ketchikan in one long day, or break it into two and anchor at Foggy Bay, as one option, or any of several other spots.
No trying to make it sound too tough - but some realistic planning is worth doing, especially for those longer stretches of more open water. We've been doing BC or SE AK most summers since 1993 - it's wonderful cruising, fishing, critter-watching, and sightseeing!
Heading up via Prince Rupert again this summer. Happy to discuss further,
