This one's going to Superman. Doctor Manhattan has a very impressive power set, but his feats are quite small and his potential/limitations undefined.
Superman tanked a supernova and survived a black hole; the Doctor has never demonstrated destructive capacity anywhere near that scale. Though the Doctor has managed to piece himself back together after being blasted into atoms, the Infinite Mass Punch would reduce the Doctor's quantum state to even more basic components of matter (see: What if Superman Punched You (https://www.youtube.com/watch?v=V-fL8zopddI).
If the Doctor could pull himself back together after that, Superman still has Phantom Zone technology and the means to warp the space-time continuum just by rubbing his hands together and using static electricity. And since the Doc was so decisively outsmarted by a mere human--to such an extent where his ability to "see time" became unreliable--Superman's intelligence and speed are arguably high enough to do the same.
