Well, in the very game, in this case MK4 because that's the game which was dedicated to their duel, I think Raiden. I mean, come on, the only moves Shinnok has there are some stupid mimics (and computer doesn't use even them), while Raiden has the whole arsenal of moves: lightning bolt, torpedo, teleport...and he even looks somewhat more muscular than Shinnok. I could hardly guess Shinnok is a divine creature judging by his combat skillfulness.
However, ignoring the games, I don't know. They seem to be equally powerful. Shinnok's status is a level higher than the one of Raiden's and so are his powers, probably. But, again, Raiden is more experienced as a fighter and in his dark version in MKD he seems quite merciless and savage.