The short answer is that if a player gets an offer from either one of these, he should take it. I believe that the players at both tend to be very happy, both with their schools and their programs. As for facilities, right now CMS has the edge. The fields are fairly similar in quality but CMS has a brand new, extremely nice athletic facility. Pomona's is pretty old, but they just started to build its replacement. I'm guessing it will be ready by the 22-23 academic year.
RE LL's comment. I actually think the profile of the average Pomona or Pitzer student and the average Claremont McKenna student is pretty similar; you'll see lots of Econ majors, government majors, some pre-law and pre-med type majors etc. The Pitzer students have the rep of being more crunchy, while the CMC students are thought to be conservative "econ bros" and the Pomona kids are more liberal. But those are the stereotypes. In real life I think they're all very smart, very motivated, very hard-working kids. The Mudd kids are a different beast. Many of them are more like Caltech players - prodigies and geniuses who happen to also play baseball. Note that they get no help with admissions, unlike the others.