The huge undulation of the waves by the rocks looks even more off-scale with the ships in place. Even if it's an arcadey game, some sense of cohesion is good to have, even if things aren't fully to scale or realistic. If you like the exaggerated undulation, why not make the ships rock with the same intensity?
Also, try having the water by the rocks undulate rather than merely raise and lower, that is, have the crest(s) pass by the rocks rather than having the entire water level drop and raise. Right now, the undulation looks less like wave action and more like bobbing because it's so uniform across the entire surface.
As for how to make the water surface look appropriate, I'm not sure what to suggest specifically, besides avoiding the latticework of highlights that suggests water caustics. Focus instead on directional highlights, since you're dealing with waves.
Potentially useful reference image? You could also have some variant tiles with a bit of sea foam (having sea foam on the detailed tile would create too much obvious repetition).
I think the rocks could do with being recoloured. Right now, they're hard to tell apart from the water at a glance because they're the same hue and value. If you want to use the same palette for them, then consider using the darker colours more and using the midtones and highlights less, so that the rocks can have a different overall value from the water.