In nearly all aspects the 2 major roof rack systems are darn near identical in terms of functionality. But in one sometimes vital way they differ. Yakima bars are round so if you have a contoured roof I think they make better contact with a boat. If it's an inflatable who cares, and if you have a totally flat roof i.ee truck then Thule may be the better way to go as you actually get a larger footprint on the boat.

Still I prefer the yakima, as I think the round bar is a smidge easier for tying random objects to. If there were a significant price difference I'd go with that in most cases.

Cheers