The ability to land in rough water is limited by the hull strength.
Pontoon type floats have struts and the struts can break. Hull type
aircraft such as a Lake use the hull itself to land on, no struts.
Although you CAN break anything, usually hull type aircraft can land on
the incoming wave's backside (the worst spot), hit and not breakup
HARDER than can pontoon aircraft. Of course it depends on the plane.
Larger planes tend to do better. But even the Beavers and such can
break a strut. Usually when the waves start whitecapping, 15knot winds
or so, small GA planes can no longer land safely on whitecapping waves.
But there are waves and there are other waves, it all depends.

Like Pete said, high wings tend to be able to get into docks better
because their wings clear the docks. Low wing planes usually wont
clear, so you can't get the fuselage up next to the dock.