Hmm...it's a tough choice:
The original is the most well-rounded, featuring a good balance between stealth gameplay, boss fights, shooting segments, story, and characters, but it's really starting to show its age.
Sons of Liberty is highly underrated in my opinion, but it's also starting to creak a little, the plot gets too tangled up in itself quite often (it's like there's no editors on these scripts), and then of course there's Raiden, who's a (slightly) better protagonist than he's given credit for, but still not even a quarter as godly as Snake.
Snake Eater has the cool James Bond vibe going for it, solid (no pun intended) gameplay, and the only story in the entire series that shows some degree of restraint. Plus, it's one of the only action games, period, that takes serious responsibility for its violence, manifested here in that chilling sequence with The Sorrow. Still, I found the constant menu surfing to be tedious and stupid, the boss characters/encounters (The End, Volgin, and The Boss excluded) are kind of meh for a series known for excellence in that category, and the lack of modern technology can occasionally prove bothersome.
And then there's Guns of the Patriots, which I'm still in the middle of playing. It's very, very, very high quality stuff all around, but the problem is that it's less of a game, more of a movie that sometimes lets you control it. Also, the story, which is sorely in need of heavy editing, ranges from breathtakingly brilliant to face-palmingly mediocre (Kojima is one hell of an auteur, but he has zero restraint and far too often, he can't write dialogue for shit); the leaping of logic and the jumping of sharks abound all over the place.
In the end, I guess that to pick a favorite, I'll have to strictly separate gameplay and story, since the series itself pretty much does that anyway. For story, I'll go with Guns of the Patriots, for gameplay, Snake Eater.