Realistically speaking, since in the world of Subnautica the animals tend to be relatively grounded (or at least try to be), I would say this is kind of a 50/50. It's basically the tiger versus lion of 4546B.
Both are equally aggressive and not exactly the smartest sea tools in the ocean shed so that won't play a part here. Both can see well in dark waters but the environment is foreign to both so that won't be an issue either, and the Reaper's sonar makes it so anything in the vicinity can hear it so it's not going to use stealth against the Cheli.
The Reaper is slightly larger but most of that is in its tail, and that grants it better maneuverability (but they're both roughly equal in speed). The Chelicerate is covered in armour and thus has better defense (though considering the kind of things a Reaper can pierce and bite through, that may not matter),
also has a bigger face and thus larger jaws that may be more potent overall, and either way they provide more reach for it (and considering Maida made use of a Cheli's mandible on her P.R.A.W.N. suit despite having a Reaper's skeleton with her makes me think the Cheli's jaws might be superior to the Reaper's, which just based off sheer size would make sense).
We don't know how they compare in-universe (one of the original unused endings had Maida using that Cheli mandible arm to pierce through and down an Alterra ship, which to me suggests a Cheli would easily be an issue if it attacked a Cyclops, same way a Reaper is) but gameplay-wise they're both comparable when it comes to the damage they deal to P.R.A.W.N. suits.
This is Inconclusive in my eyes, I feel like either one could win this.
