I'm not with Laminar Research, just a fellow simmer in the UK, but once you've loaded your seaplane aircraft onto a body of water, click on the 'flight configuration' option, then click on the customize button in the weather section, then check 'wave height' under the heading 'Bodies of Water'. Please see photo below for guidance.
I had my wave height option simply set to 1ft and the aircraft bobbed about all over the place!!
There is one other thing that I haven't been able to fix yet, and that relates to aircraft movement across the water surface, even though there's no wind blowing??
Hope this helps