Didn't play V yet.
MGS3 has the best overall package from gameplay, to story, cutscene direction, soundtrack, etc.
But MGS2's last ~1.5 hours is the peak of the series. Best twist, favorite last boss fight, and favorite ending. The game's messages extend far beyond the game itself, which is one big way it has a leg up on MGS3 (and the rest of the series, though the first game is kind of close).
Mega spoilers (really really wouldn't recommend watching before playing MGS2 yourself...it's worth it. This is one game I'm glad I wasn't spoiled about beforehand.)