Right now winning Golden Boot or being highest rated player for a season has no upside other than bragging rights.

Recommendation:
At the end of the season, the Top Scorer should get +15% on shooting and finishing attributes, Top Rated player should get +15% on one each of the Defense, Attack, and Physical attributes of the managers choosing (i.e. I could pick to add 15% to one of the Defense attributes, one of the Attack attributes, and one of the Physical attributes), and the Top Assists player should get +15% on passing and creativity.

To compensate for increased abilities (and for realism), each of these players' salaries should go up by 15% as well.