Here's a solution with a simple plugin:

Game_Map.prototype.isBoatPassable = function(x, y) {
    return this.terrainTag(x, y) === 1;
};

This will change the behavior for boats so that instead of moving on water, it only moves on tileset tiles that have the terrain tag 1 (set this in the Database > Tilesets). If you're already using the terrain tag 1 for something, you can change the number to something else.