They are, for all practical intents and purposes, the same. They both work great and look great.
That said, I have a Thule roof rack, with 2 fork-mount carriers and a kayak stacker. Most of Thule's products will fit on Yakima or Rocky Mounts bars, so that is a plus (I have a friend who has a Yakima, and sometimes it is necessary to put my Thule carrier on his bars, as he only has 1 carrier).
Yakima carriers only work with Yakima bars.