Well..... I say Shinra Tensei is a balance move, it can be used offensively and defensively, however bijuu dama is completely a long range offensive move, unless Naruto makes a super mini bijuu dama which he can use up close. so for attack purposes bijuu dama, for a more versatile usage the shinra tensei.
Nagato used extreme Shinra Tensei (the one which destroyed Konoha).
Who would win?
Because once Bijuu Dama experiences a force on the opposite end, it will explode. Obviously Shinra Tensei provides that force and Bijuu dama will be helpless. The bijuu dama will be set of and Naruto will be caught in it - that is if he doesn't escape; Nagato on the other hand will be left unscratched.
Naruto used Bijuu dama on fodder #939458
After the explosion, there will be nothing left of the person. Nada. Nuffin. Nu uh.
Nagato uses extreme Shinra Tensei on the same fodder.
There is a high possibility the fodder will die because his body cannot cope with the force and will break his spinal cord etc... However there is still the small possible chance that the fodder will get lucky and survive, though they'll be in comma or would be seriously physically disabled.