"The SNES era really stands out to me as the high-water mark for JRPGs"

I'd have to put the high-water mark at the PS2. The PS1 era was confused, but they mostly figured things out again for the PS2.

That said, the genre remains alive and well anyhow. Once everybody but Square accepted that you don't need to try to make every single one a graphical extravaganza, they picked back up again. (I don't know what I'd call the flagship series nowadays but I can tell you it is not Final Fantasy anymore.)