Those are molded ABS pods which really isn't that 'live' of a material. I don't think that is your core problem. However, you could still try a little damping (HushMat, DynaMat, RoadKill, etc.) attached to the interior wall of the pods. It may make a marginal difference. A solvent-based spray expansion foam is highly effective in killing any resonance. Contrastly, a latex foam product will not stick to the pod interior and is useless. Easy does it as you would not want to reduce the pod's interior displacement with too much foam. You could also fill the pods interior with polyester fiberfill which will convert some of that acoustic energy into thermal energy which serves to attenuate the interior radiation. But too much of a good thing will take the spring out of the midbass and leave the sound a little flat. Its a trial and error thing.
If you have a flat cast tower rather than a tube tower you get alot more radiation reflected into the boat.
If you have multiple staggered speakers then some forward speaker radiation gets reflected of the rear most speaker.
Plus, if your tower is forward leaning and/or lower than normal then the problem gets worse.
If you have one pair of speakers always take the highest position.
An EQ can help attenuate the frequencies most radiated into the boat or at least the spectrum that you or your occupants are most sensitive to. The Wetsounds EQ has separate circuits for the tower and in-boat zones so you don't have to influence the in-boat speakers as you are affecting the tower speakers.
Beyond that there isn't much you can do about the major causes when you are pushing the tower speakers hard to reach the rider.