Lots of things to consider. If you're by yourself, then consider the smallest sea kayak that you can find. Many have waterproof storage hatches right under your hands, and the good thing about this is, after shooting, you almost *have* to put the camera away -- there's no place else to put it..
I personally prefer canoes, and have had several in my life (and I once solo-paddled the length of the Mississippi River, from the headwaters lake to the Gulf of Mexico.) The problem with canoes is that they're wonderful when you're canoeing, but you can get in trouble if you're deeply distracted by something like photography -- that's especially true when there are two people aboard. For example, if you come across a point and suddenly see a bunch of wading birds on the lake, and both you and your partner shift your weight at the same instant, to shoot the birds, you can find yourself rather quickly in the water. Furthermore, a canoe is big enough that you tend to put the camera in front of you, *on* its waterproof bag, rather than in it, for instant access. You can lose a camera that way, since most don't float that well.
An advantage of a canoe, that you can never do with a kayak, is that you *can* -- very carefully, and after some practice -- stand up in them in flat water. Just getting the camera up five feet can make a radical difference in perspective.
You can carry a lot more in a canoe, but if you're mostly going to be on local lakes, that's probably a non-issue. You can also carry a canoe into small lakes where there are no landings, but you can do that with a kayak, too. I mention it because there's a third alternative. If you go to a big boat place, you can find very small aluminum row boats, dinghies, which also can be portaged short distances, and carried on a car top. You can then either row them or use a small electric motor or even a sail, and they are more stable that a canoe, and carry as much. Like this:http://www.ghboats.com/10_dinghy.shtm
I haven't had a great deal of luck finding compelling shots on the water, but YMMV. One time, however, a friend and I, in a canoe near the headwaters of the St. Croix River, floated into a herd of whitetail deer which were standing at the edge of the stream, drinking. They apparently didn't recognize us as human, as we sat motionless in the canoe, for we virtually floated into them before they broke away.