The NES games are main series, the MSX ones are. The NES games are none-canon offshoots that Kojima had nothing to do with. They're also shit.
Personally, I think they're (the MSX games) are quite fun, but you wouldn't need to play them for plot reasons, the entire story is revealed throughout the rest of the games.
You're probably best playing the games in release order, but it's up to you, really. In terms of story, it makes the most sense played in release order but, personally, I don't think the story is really all that great. Still if you're looking for a definitive "play-order" release order is probably the best.
In terms of gameplay, I dunno what order I'd recommend. MGS3 represented a marked shift in style; MG1 through to MGS2 are all quite fast-paced, almost arcadey, takes on the stealth genre. MGS3's more open ended environments, the focus on camouflage (and thus, hiding in plain sight) and the added ability of guards to hear you when you run up behind them makes it a much slower and more complex game. Which you prefer will largely depend on you, but most people agree MGS3 was also a big improvement.
Some people would also recommend release order because of gameplay improvements but, personally, I thought MGS4's gameplay was just awful. Still, you might like it and since the game has 9 hours of cutscenes that barely make sense without having played the rest of the series, it probably should be the last you play before MGSV.
Also related, while I think MGS2 improved on MGS' mechanics beautifully, the level design is a *lot* worse. MGS2 is still worth playing because of how ahead of its time it was in some respects. For instance, enemies can see your shadow! I can't think of a single other stealth game that does that.