For me, it's a toss up between Ed Bernds and William Beaudine. I'm
tempted to give Beaudine the slight edge. To be fair, though, Bernds
wasn't with the boys as long, if he had started with them earlier or
left later he could very well have made many more great films with the
boys.

Bernds (his best, IMHO)
Clipped Wings
Private Eyes
Bowery Boys Meet the Monsters
Spy Chasers

Beaudine (his best, IMH0)
Jinx Money
Smugglers Cove
Blues Busters
Let's Go Navy
Ghost Chasers