Snake would win completely, Sam might have a bit more slim stealth skills but in a hand-to-hand fight with Snake he'll get owned like hell. Sam has problems taking down 2 average security guards in a police station lol, and Snake takes down an Metal Gear lol. (And guys this is referring to Solid Snake (MG1, MG2, MGS1, MGS2. Not Big Boss from MGS3)
I would say that Snakew would win in hand to hand combat, but I still think that Splinter Cell is a better game. I mean you can go through the entire game without firing a single bullet if you want to. His stealth skills are unmatched by anyone. I do agree that Snake has better hand to hand combat skills though. Plus anyone who has read the Splinter Cell instruction manual knows that the night vision goggles and the light on his back are there so the player can see him because some people play with their brightness lower to get the full pitch black effect and it's impossible to see Sam which makes it pretty hard to grab someone from behind without bumping into him.