MGS 3 by a comfortable margin.
I've got a soft spot for MGS on the PS1 though. At the time it was truly revolutionary.
MGS2 get a bad rap for obvious reasons, but the gameplay was a proper evolution and tight as hell, regardless of how fucked up the story was.
MGS4 had some good things about it, but it really took the cinematics a step too far. I also didn't care much for the story and environments. For an early PS3 game though, it still looks rather amazing.
MGS5 is a mixed bag. The story is nearly impossible to follow, given that it requires you to listen to hours and hours of audio tape to really comprehend everything. The gameplay is second to none though. Overall though, I don't think making a bigger version of "Peace Walker" really worked. Peace Walker had so many extra things to do in terms of base management, in order to hide it's technical limitations in the actual gameplay department. It all worked really well with it's bite sized maps, in that you always felt like you were accomplishing something, even if you only played it for ten minutes. Taking all the elements from Peace Walker, and then adding it to huge game, kind of made all the base management stuff a little tedious.