Duck Dodger,
The first question is what sort of water are you planning to operate in - is it protected water or open water. Protected water means inland water, or water contained in a reef. Open water is generally associated with salt water, but large lakes and waterways frequented by boats can have similar charactaristics.
In rough water nothing beats mass - float length comes second, followed by power, stol performance and structural strength. What they do with Twin Otters (5700kg MTOW) in the Maldives demonstrates this well. The Caravan (3800kg MTOW/675HP) copes with rough water well if kept within its limits, but they have a high stall speed and a firewall is very unforgiving to mistreatment (ie $$$$$$$). The Dehavilland Beaver (2500kg MTOW/450HP) copes with rough water very well considering that its MTOW is only about 2/3rds that of a Caravan - its STOL performance and strength help overcome its lower mass, shorter float length and limited power. In the Whitsundays 206s (1600kg MTOW/285HP) fell out of favour because they couldn't cope with the water - it was too rough for them too regularly.
The second question is if you need an amphibian or will a straight floated aircraft do the job. The undercarriage system on an amphibian is significantly heavy - some models of amphibious floats can be around twice the weight of straight floats. Additionally the openings in the floats for the main wheels also detract from the takeoff performance. From a performance perspective (not rough water perspective) for the same load you will be able to use a smaller aircraft that is on straight floats.
Generally tail wheel aircraft make better floatplanes than nose wheel aircraft - the loads imparted by the floats onto the airframe is in a similar position to the main gear on a tail dragger.