So I have come up with (not saying I'm the first) an interesting way to make choppy water. You need a sheet of the blue foam insulation board available at Lowes or Home Depot. You can make this as big or small as you need. Here is the technique I use.
Cut out the approximate size you need and lay it down. Now, dig into the foam using a flat head screwdriver a few mm or whatever you feel, just don't go all the way through! I find about a quarter to half way through produces the best results. You aren't cutting out the chunks of foam, you are breaking them off. When done right this produces what I think is a very realistic water look! Now, some chunks will be a little bigger and others smaller, just practice and don't worry about uniform results as choppy water is not uniform! Generally keep doing this in the same direction each time.
Once this is done you can cut out the areas boats or items will go to create a partially submerged look. Now for painting just mix up your colors of blue or blue green. Then you can use a brush with white on it, just a little paint on a large brush, and swipe it over the sheet of foam so that it really only hits the peaks and it creates a wonderful whitecaps look!
!!!WARNING!!!!
You might want to wear gloves using this method as I got blisters both times due to the repeated steps from the screwdriver and the foam board.