Both are longtime reputable brands so take that out of the equation. The Yakima FatCat is the best rooftop ski/snowboard rack currently on the market, PERIOD. I've owned several different styles over the years, and it is definitely the best thus far. Wider than others to accomodate even the widest of boards or as many pairs of skis as you want. Also the most low-pro and aero option out there to minimize MPG loss and no windnoise. Also called the Whispbar WB300. Cargo box is definitely an even better option, although much more costly and more MPG loss.
16 NS West . 15 NS Snowtrooper Brother in Arms Edition . 13 Salomon Pow Snake
15 Now Drive . 14 Burton Genesis
14 Flow Hylite