It's to tough to call, I'd lean towards the German boats, However the Japanese never put the resources into their anti submarine warfare capabilities that the Allies did.
Their merchant fleet was almost non existant by 1945 mostly due to the success of
american submarine forces. But then again without the allies staggering investment in aircraft and new technoligies the U-Boats would almost have certainly closed the atlantic.
The US subs seemed to be more a bane to Japanese fleet as well.
They sunk the Shokaku and Taiho at the battle of the Phillipine sea
Archer Fish Sunk the largest aircraft carrier of WW2 the Shinano it's first day out of port.
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