If you have the time, equipment, and skill, nearby Kuiu Island (pronounced Q-U) provides excellent kayaking and canoeing opportunities. Two wilderness areas encompass the south and west sides of Kuiu; other parts have been heavily logged. Dozens of interesting islands, islets, and coves crowd the west side of Kuiu in the 67,000-acre Tebenkof Bay Wilderness, while the south end includes the 60,000-acre Kuiu Wilderness.
The Forest Service publishes a detailed map of Kuiu Island with descriptions of all portages and routes. Get a copy of Kuiu Island/Tebenkof Bay Canoe/Kayak Routes from Petersburg Ranger District (907/772-3871, www.fs.fed.us/r10/tongass [1]).
Experienced kayakers will enjoy the paddle between Kake [2] and Petersburg [3] around the south end of Kupreanof Island. There is open water in places, but a good portion of the route is protected, and the state ferry makes it easy to get between Kake and Petersburg.
Links:
[1] http://www.fs.fed.us/r10/tongass
[2] http://www.moon.com/destinations/alaska/southeast-alaska/petersburg/kake
[3] http://www.moon.com/destinations/alaska/southeast-alaska/petersburg