The really important thing to bear in mind is that with a canoe/kayak you have a very easily driven hull, that doesn't need much power to propel it, and you also need to keep the weight down, as reducing the weight reduces the wetted area and so reduces the power needed.
A reasonably fit paddler can deliver a sustained power of around 50 to 100 watts. If you only want to go at typical canoe/kayak speeds then this is the sort of power level your looking at. As power determines weight to some extent (more power = heavier batteries for a given endurance) it really pays to look long and hard at efficiency.
You have several options, here's a list with some typical propulsive efficiencies:
Paddle boat type system - typically around 40% at best, unless you make the paddle wheel diameter quite large, when you might get it over 50%.
Air propeller - A big diameter (around 4 to 5ft) air prop might get you up around 65 to 70% efficiency, if you turned it slowly and carefully matched its pitch to the needed power.
Water propeller - Efficiency will depend on the number of blades, prop diameter and blade loading. The fewer blades the better, the bigger diameter the better and the slower rpm the better, as a general rule-of-thumb for this kind of boat. I;ve tested a few props for a very similar project to yours (see the electric boat thread) and have found that an 8" diameter x 6" pitch two blade marine-type prop was only about 40% efficient. My current prop is a 13" diameter x 12" pitch prop that looks just like a model aircraft one. Its a bit over 80% efficient.
A Thai-style long tail drive will work well and is simple to build. Use a low Kv motor and a reduction drive, perhaps using off-the-shelf HTD toothed belts as I've done, and a model aircraft prop (something like a cheap APC 12" x 10") and you should get much better results that using a trolling motor.
You might want to look at just changing the prop on a trolling motor for a model aircraft one and seeing how it works. I have a long thread running on the Boatdesign forum where one member, McDenny, has done just this with pretty good results. See here: http://www.boatdesign.net/forums/boat-d ... post302305
Please ask questions on the forum, rather than by PM, as it helps others and you'll get a better range of answers.