I like 'em both but prefer to be on the water instead of alongside it. That way, if the spot I'm in isn't working, it's faster to get to another (and lots of places out here really can only be reached on the water).

For small lakes, I like my kayak but a flat bottom boat is fine too (except I don't own one of those and I do own a kayak so I tend to fish from it a lot more often than anything else).