This is a difficult question for me - At his peak, Mysterio is my favorite, but it's a small window (94-second knee injury in 98). Eddie did it consistently for more than a decade. It's like Beatles or Stones; There is no wrong answer.
I chose Eddie because of is evolution as a wrestler and character over his entire career. He could wrestle in any style, heel or face. Did it in Mexico, over in Japan, did it in ECW, then in WCW, then in WWE - all while adopting to the style and audience of the promotion. And
he took a little from each place & time in his life and incorporated into his moveset and character. And
he was innovative as shit inside and out of the ring.
That said, Rey may go down as the "Greater" of the two because he broke so many walls: Luchadore, undersized, doesn't talk well, high flyer, etc. And say what you want about his inability to "draw" but I guarantee you that his mask, individually, is in the top 3 or 5 best selling piece of WWE merch ever marketed. I'd also bet his action figure is/has been one of the top 5 sellers as well for the better part of a decade. And of course that he's created probably a dozen or more spots that people still use today, and a couple nobody else has been able to do before or since.