Best is probably Thief 2, my favorite is Chaos Theory. Chaos Theory offered such a great package, amazing single player campaign with great levels, really fun and innovative co-op campaign and an awesome Vs. mode with Spies vs. Mercs.
Thief 2 though, compared to it's competition, was essentially untouchable. There wasn't other games like Thief 2 and they essentially created the immersive stealth genre with nobody else to learn from or emulate.
MGS2, while amazing for it's day, just felt like stealth wasn't very well done. I LOVED MGS2, it's crazy as balls, and it was STUNNING in regards to pretty much everything else released around it, but it's A.I. was not very well done and it just didn't do stealth as well to me. When I think about MGS2 I think about it's crazy attention to detail and insane characters and forward thinking story. Last thing I think about is stealth.
Thief 2 gets my vote. Not my favorite of those options(again Chaos Theory) but def. the best at pure stealth and immersion.