I would think a Particle object that you then animate it's motion with the particles being bubbles and have them set to 'Free' would work out. Give them plenty of 'Life' so that they survive long enough to work, and set them to have a slight negative 'Z' gravity setting so that they float up in the water.

As far as a wake on the surface, LOTS of people have tried many different methods to create a wake. The best that I know of involves creating a 2d video, then using it as a displacement map on the surface of your water.

Let us all know how it all works out for you!