I generally shoot ISO 100, 1/2000 @ f4 for bright sunlight. As the sun goes down I will drop the shutter speed slightly but not less than 1/1000. At that point I will increase the ISO to compensate for the loss of light.
Increasing the ISO will allow you to continue to shoot with the same settings with less light. Decreasing the shutter speed will result in more motion blur due to the high speed movement that is inherent in wakeboarding. How high you can increase the ISO and still get good results is dependent on the camera. Most are able to go to ISO 400 without grain/noise becoming too much of an issue. I've shot ISO 3200 with my new camera (Canon 1D Mark II) and the results were acceptable after running the image thru a noise reduction program such as Neat Image. Here is an example of a shot taken right after sunset at ISO 3200 1/1000 @ f4 after using Neat Image and resizing for the web with minor sharpening applied.
and here is a 100% crop before noise reduction (no changes to the image except to save it at 50% quality jpeg).