I've dived at the Yonaguni Monument, and one thing that's usually not clear from breathless hype like this article is that the site is both quite deep (mostly 10-30m underwater), a fair distance from the shore (hundreds of meters, IIRC), and that said shore consists largely of steep cliffs.

I've yet to hear even the most rabid "lost continent of Mu!!!1!1" enthusiast propose any sort of plausible mechanism to explain how a manmade monument could somehow have moved hundreds of meters diagonally from above sea level into the bottom of the ocean without getting completely destroyed in the process.