In a comic, Superman would win. Superman is the symbol of the company and they wouldn't ever let Flash, one of their B-listers, straight beat him without plot contrivance.
Logically extrapolating their abilities, Flash should win. Superman has no counter to phasing or Speed Force BFR. And that's just new-52 Barry. Wally is even further out of his league, as even Jay Garrick has speed stolen Superman to beat him (in a race, admittedly) and Wally is the master of speed stealing. Wally's punches would definitely hurt Superman, as they have destroyed Anti Monitor armor, KO'd Mongul (who has similar durability to Supes) and KO'd Martians. And, as always, superman has no counters to Wally's phasing. Wally can also "reverse fly" by running faster than exit velocity and just running out of the atmosphere and into space. New-52 Barry has stated his explicit weakness to flying in JL, though his Speed Force BFR would probably render that moot.
That said, in Superman's encounters with the evil Reverse Flashes, both times Thawne and Zolomon straight embarrassed him and a few other JL members who were with him, so there is atleast some precedence to the point that Superman would have a hard time dealing with someone so fast.
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