>>125448233REX shoots a warhead, not a missile, from the railgun. RAY doesn't carry nukes. I assume Peace Walker and Zeke shoot from those long-ass guns they have, but I'm not sure, I haven't played enough of Peace Walker to know.
RAY would probably win. It was specifically designed to destroy Metal Gear REX and its knock-offs, and ZEKE and Peace Walker aren't as advanced as REX.