The accident occurred shortly after 2.30pm near the Romanshorn port on the Swiss side of the lake, Thurgau cantonal police said in a statement.
According to the police, the father left his son helming the rental boat.
The four-year-old made a sudden change of direction and they found themselves in the path of a ferry.
Although the father then tried to change direction again, and the ferry also took steps to avoid the rental boat, the two collided.
The man and his son were slightly injured and were treated in hospital.
The rented motorboat suffered around 3,000 francs of damage but the ferry was not affected, said police.