Considering Sam didn't have much of a cyborg body to begin with and completely dominated Raiden.
If by completely dominated you mean used one of his strongest possible attacks that all his upgrades and gear optimized with the strongest weapon in the game to hit Raidens only real weak spot while Raiden was holding back, then yes he dominated him. Could have been worse I guess, he could have been captured in battle twice by women like Snake...
Fun fact: You're wrong. It's canon that Raiden is superior to Snake, even without taking the whole cyborg thing into account.
You're very wrong. Raiden is my favorite character from the MGS series, but Snake had more "raw" skill then Raiden, however, Raiden from MGR:R VS. Solid Snake (any MGS game) would most likely destroy him. But then again, keep in mind, Snake did defeat (not kill) Gray Fox in MGS1. And if you read the "body" description of the Gray Fox body in MGR:R, it CLEARLY states that the Gray Fox body IS just as good as modern cyborg technology in the MGR:R era.