Reaper counters mercy in almost every way. A good ult from him will kill her as well, meaning she can't revive. When ultimates aren't taken into consideration, reaper deals damage extremely fast, meaning he can take out enemies much faster than Mercy can heal them.
With the exception of ultimates, I generally disagree. Mercy is just barely mobile enough to avoid getting hit by big meatshots from Reaper. Against many other targets, Reaper reallllly wants to be able to kill in as few shots as possible, since he's vulnerable when he's in kill mode. Forcing him to take 1-3 extra shots against whoever is being healed can be what it takes to turn the tables.
The only reason why I might agree with negativity vs Mercy, is that Lucio's right click to deny Reaper aggression and speed boost to deny Reaper disengage is so much better at being a pain.
Well. This site shouldn't ask 1x1 counters. But Team oriented counters, because Mercy is one of the greatest counters to Reaper... As soon as reapers ults, Mercy can revive all allies that he killed. Her ultimate denies and grant a lot of Victories this way. A Mercy ultimate is a nightmare that any Reaper fears. As long his ultimate don't get her, of course. :)
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The only reason why I might agree with negativity vs Mercy, is that Lucio's right click to deny Reaper aggression and speed boost to deny Reaper disengage is so much better at being a pain.