EDIT:
THIS SHADER WENT COMMERCIAL AND CAN BE DOWNLOADED FROM THE ASSET STORE.
(If you were lucky enough to grab it previously, you are free to use it anyway you want but i would appreciate your support if you buy it before using in a commercial product.)
First off, I love your idea of using screen waves for and underwater effect ^.^
The only thing about the shader that bothered me was that the waves bunch up on the left-hand side of the screen. The longer the effect is active you get more and more waves piling up on the screen. This may have indeed been the effect you were looking for, but as the player spends a good deal of time underwater for me, the effect was to dramatic.
I made a slight modification to the shader, adding Time instead of multiplying it.
Thanks again for this idea 
-Snip-
For underwater scenes, i would suggest you use this one
http://forum.unity3d.com/threads/76573-post-processing-wiggle-shader