I was there in 1992. I didn't paddle, but I do recall that there was an area designated for canoe tripping - similar to a Quetico trip, portaging between lakes. South of Anchorage on the Kenai peninsula. Found the following with a web search for "canoeing in alaska" , and it might be one or another of these that I am thinking of.

"The Swan Lake canoe trail encompasses up to 30 lakes and 33 miles of river. The Swanson River canoe trail ancompasses up to 40 lakes and 46 miles of river." near Soldotna.

"We highly recommend for unguided tours the purchase of the book: "The Kenai Canoe Trails" by Daniel L. Quick. Northlite Publishing Company. The book has in great detail: maps, a description of campsites, lake descriptions, fishing information (what fish are in what lakes and how to catch them) and wildlife viewing information. Visit their website at   (You need to Login or Register

The guidebook above would be a good start. I spent about six weeks in Alaska, and don't recall ever seeing anyone canoeing. The river trips that I have read about all seem to be rafting trips, and drift boats were the norm for fishing. People who live along the rivers use motor boats or jet boats for "commuting". One thing for sure, is that the rivers were all full of glacial silt, so you would want to have a bucket to allow silt to settle before filtering your water, and probably bring an extra filter cartridge.

a couple of other resources you might want to check out would be the Alaska Milepost book - an annual publication with info on what is along all the highways, has current info on highway construction, what to do and see, etc., and gives you a good "thumbnail sketch" of what you will find along the highways. Alaska Magazine would be another good resource - you might find a website for them, and see if they have any articles on canoeing areas that might be of interest.