I think Sam has the slight edge in stealth. He's the one who's shown ninjistu-like maneuvers in stealth. Thing's like wall splits, upside down neck breaks and marksmanship.
Using his winch to infiltrate building from the outside through the windows or come down from rooftops like a spider.
Also let's not forget that Sam has a satcom, which connects to satellites giving him a view of human beings in an area. I don't know if Snake's tech protects him from thermal vision.