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Easily Superman Prime.
Think of it ....Superboy prime has done amazing feats, but Prime Superman is the strongest version of Superman ever.
Also note that he granted his strengths to the various supermen of the future (eg Superman 1 Million) through his covenant, and thus augmented their already potent powers.
Superman 1 million punched through time to arrive 85,000 years into the future, and he did this when he was almost out of all strength due to being too far away from the SuperSun (where Prime Superman was, granting strength).
If Superman 1M can have such power (to punch 85,000 years into the future, and do so when he has so little life essence left that he has turned into an old feeble man), just how powerful do you think Prime Superman is?
Now, obviously SBoy Prime is no pushover ....the guy blitzed flashes, and he punched out of the phantom zone. However, someone who can punch 85K years into the future (SM1M), and do so while operating at zero energy, can replicate what SBoy Prime did (and I believe that SM1M could also blitz the various Flashes, since he is far faster than normal Superman).
And if SM1M can do all that, and do it at a thoroughly weakened state, then just what is SManPrime capable of? SMPrime would whoop SBoyPrime a new one.
And it says in the comic that when he arrived after his many years wandering through space, that he was already powerful beyond belief. And this was BEFORE he spend a millenium in the heart of the sun.
SBoyPrime would get owned by Superman Prime in the same way SBoyPrime owned Kon-El Superboy.
10/10 SMP.