Transport Juveniles.
A fully grown adult dinosaur would require an independent barge as other answers have suggested. The An adult dinosaur would need to be kept sedated through their food or water. In addition, they would require significant care to ensure it's survival in their sedated state and protection from the elements while at sea.
It would become easier if you are transporting juveniles instead. They can be kept in iron cages on the main ship instead. They would require less food and management than an adult.