MGS for sure. It trumps SC in almost every way. Storywise SC has a more gritty realistic one that seems is more enjoyable from a serious standpoint. MGS also has a great story but has too many "lame" anime moments that break the mood for me. MGS still has a lot of cool story elements nonetheless.
Gameplaywise MGS kills SC. It's a difference between japanese and american game design. In SC most of Sams actions are done through toggle or quicktime events. IE: hit the A button to grab the guy then push another button to peform the next action. MGS give you more control over the character actions. Wih snake you have to perform a sequence of button pushes, stick moves, button holds, and pressure sensitive functions to grab an enemy and do whatever action afterwards. Its more like mario where you have supreme control over your character's actions.