He has mentioned a few times that "War Horse" is a very special book for him. It was his first foray into writing for adults and it became an international phenomenon.
However, he has also expressed fondness for other works, such as "The Butterfly Lion" and "The Amazing Story of Adolphus Tips".
Ultimately, it's hard to say for sure which book is his absolute favorite. It likely depends on the day and what he's feeling at the time.