Yellow Jacket (E-Tech SMG)
Shoot the Electric Coil Barrels on his back since those are the source of his power.
Once you destroy one of the coils he runs away and activates a shield, then some Loaders will spawn. While Jackenstein's shield is active he is nearly invulnerable so focus on the robots (use corrosive weapons against them). Then Jackenstein comes back down, destroy his other barrel. He runs again to a cliff and activates the shield, again wait for him to come back, when he comes back then just aim for his chest (critical spot) and finish him off.