It was stated that Goku could have obliterated Pure Boo if he had been able to powerup as SSJ3 -- but due to the stamina restrictions of his mortal body, he was unable to.
Conversely, Janemba was demonstrably superior to SSJ3 Goku, despite Goku being dead at the time, and therefore possessing a spirit body that didn't have the same stamina limitations of his mortal body. In fact, SSJ3 Goku ala Movie 12 is likely the closest thing to a 'full power' SSJ3 that we've ever seen.
That said, I personally have Janemba above Pure Boo, but below Super Boo.