Do you have a water simulation?
My suggestions are
fake it with springs. Each vertex on the water surface is coupled together into a spring mesh. Pull one down and they all start oscillating. You could constrain x,z motion and only allow y (or up/down motion)
fake it by summing sinewaves of different amplitudes and frequencies. Some thing like this:
rez = 32; for(i=-rez; i<rez; i++) for(j=-rez; j<rez; j++) { yofs = 0; yofs += 1.0 * sin( t + j*0.5 + i*0.125); yofs += 2.0 * sin( t + (rez-j)*0.125 + i*0.25 ); yofs += 2.0 * sin( t + (j)*0.125 + (rez-i)*0.125 ); yofs += 0.5 * sin( t + (rez+j)*0.125 + (rez+i)*0.125 ); glVertex(i/rez, yofs, j/rez); }simulate the 2D wave equation, this can be very fast on the GPU. See this page for a java applet and some pseudo code. Also check this version, the same but even simpler. A processing sketch with code.
From the wave equation sim you can get the direction (dx,dz) of the wave is traveling in
dx = h[x-1][z] - h[x+1][z]
dz = h[x][z-1]- h[x][x+1]
where h a 2D array with the height of the wave at [x][z]
You could add this to the boats position to make it travel with the wave... I've tried, but the movement becomes jerky, so I smoothed it out with a simple 3x3 box filter (smoothing the differences/velocities dx dz)
