Kind of crazy to be thinking a bout yaks with the weather you guys are getting wacked with.
First, I would suggest you get cost effective flats boat instead like a Mitzi Skiff or on of the Carolina Skiff flats boats...
That being said - I checked the Bass Pro web site and saw that they only carry the two brands you referenced. Off the cuff, I say Perception since they've been around forever.
Sit on top or covered yak?
If you and clietns will be getting out and wading - go with a sit on top. Check out the specs on the Perception site for the Bimini at 15' and the Nepali at 15.5'. The longer the yak, generally the faster it is and I like speed when I'm paddling.