Canoe has generally more storage and space than a Kayak. You also have some ability to move around in it. If fishing two from a canoe, you can actually gain some help in landing fish, and or just in general. Some expectation of staying dry.
Kayak, you have every expectation of being wet (at some time or another). You are very much 'down in the water' - some could consider this an advantage, others a disadvantage. Highly manueverable. The new Hobie Fishing Kayak (made famous by Hank Parker), is really slick looking. Now being carried by BPS (saw one yesterday), but they get TOO MUCH for it there ($1,500.00 or thereabouts).
If I was to choose between a canoe and a regular Kayak, I'd probably choose a canoe. Between a canoe and the new Hobie, the Hobie.
Tex