Artist's acrylic gel medium has been my go-to for ocean bases for a long time, but that is basically as many layers of gel on the display case base as it takes to get the wave height I want, not what you are describing. I prefer the clear to the opaque gel because you can get a much richer range of colors as you build the color up with each layer of gel.
Calm water obviously takes one or two very thin layers to complete the base; 50-foot waves in the North Atlantic in winter takes a LOT of thin layers (and can take for freaking ever to dry).
The medhod of building what amounts to a shadow box with glass sides and a glass top for the water surface was the subject of an excellent article by the legendary Bob Santos in the June 1987 FSM. He used the colored rippled-effect acrylic plastic that is commonly used in "fancy" house windows. Sounds like just what you're after.