To be fair you would have to factor in the fact that Sasuke has the Sharingan(which must be there for the chidori) and that would more or less give him the win no matter the difference of strength of the two jutsu. Though I belive that Jiraiya's technique will be stronger than the Chidori it is just the desparity between the two people(they fight differently and both are good but not against each other... imo).