I think until more of Big Boss' and The Boss' exploits are expanded on you kind of have to go with Solid Snake if only because of sheer numbers. I will say this though, Big Boss' mission in MGS 3 was tougher than any one mission that Solid Snake has gone on I think.
Big Boss was thrown off of a bridge, spent a week in ICU, went right back out on mission immediately after waking up, didn't have nano machines or much any technology helping him really, went through far worse torture, had an eye removed and managed to finish the mission without said eye (which is a big deal considering having only one eye will play hell with your depth perception), and to top it off he had to kill the most important person in his life with his bare hands. I think Operation Snake Eater stands alone as far as big time missions go.
Big Boss was thrown off of a bridge, spent a week in ICU, went right back out on mission immediately after waking up, didn't have nano machines or much any technology helping him really, went through far worse torture, had an eye removed and managed to finish the mission without said eye (which is a big deal considering having only one eye will play hell with your depth perception), and to top it off he had to kill the most important person in his life with his bare hands. I think Operation Snake Eater stands alone as far as big time missions go.