i fish both. canoe's are more stable, have more room to stretch arms/legs/back, and you can spread ur gear everywhere, fit coolers with lunch, can take a buddy out, have option to add a trolling motor for bigger bodies of water, has oar locks so i can paddle easily (like a row boat). the wind blows my canoe a lot more b/c the sides are higher so i need a slightly heavier anchor. if given the choice i would fish my canoe exclusively (i cant fit it into my apartment so i had to buy a kayak that would fit up the stairwell). i like the canoe for full day fishing trips. i can stand up to fish, stretch, or take a nap...i never need to go to shore.
my sit in kayak is more close quarters, solo use, paddles faster, better for tight or shallow streams with rocks/obstacles. the kayak is great for half day/quick fishing trips. i can't stand up in mine so i usually paddle to shore during the day to stretch and eat lunch. both are same load on/off my car. if you want to take a buddy sometimes get a canoe. anythings from dicks or sports author is fine for a 1st canoe. also check ur local craigslist for 'radisson' or 'sportspal' canoes. they are made for fishing, constructed from lightweight aluminum like airplanes so they are very light (but dent so no white water rafting), have oar locks for rowing, and the floors are lined with foam to buffer noises like moving around or dropping a lure. http://www.castlecraft.com/sportspal_wide_transom_canoe.htm
good luck and let us know how you make out.