Objectively, Square clearly has the bigger impact. Final Fantasy alone is of far more importance to the JRPG genre than anything Atlus has done. On the other hand, while Square has older importance, I'd question their modern status in comparison. I can't say for sure, I've only played two Atlus games (Tokyo Mirage Sessions and Persona 5 that I'm still playing), but Square has some big issues over the years with some of their biggest games. Final Fantasy 13 was very polarizing, 14 was a disaster at launch, and 15 languished in development hell for years and even when it did come out, it had some very clear issues. I can't say I've heard the same for Atlus and people are nuts for Persona 5, so they are in a pretty good place right now.