Thanks for the pointers! Sprites would be ideal indeed, except I don't have control over the graphics part, they are given to me as is.
I've made attempts with displacement maps and turbulence, but still not happy with the result. The displacement map using a ripple map produces ripples that are shown onto the boat at the beginning of the tween which is not pretty and it ends in a stutter. The turbulence animation is great at the beginning but goes way to fast in the middle of the tween so that it doesn't look like credible water...
Actually, an effect like this one would be perfect : http://srufaculty.sru.edu/david.dailey/svg/waves.html (with these values : frequency 12, scale 32, rotate 246). May try to replicate it.