I reckon Snake met the Colonel at least once while he was in Fox-Hound he must have met him, besides I doubt the technology existed then. But Raiden has never met the Colonel, I'm pretty sure of that. Remember the S3 Plan (is that the right name?) was meant to re-create Shadow Moses, as close as possible to train potential Snakes. So Raiden "passed" and he's probably going to work aside Snake against the Patriots.