I never had an N64 so I never got to play OoT until two years ago. That said, I have no nostalgic attachment to the game whatsoever. Still, I had a hell of a time playing it. The great dungeons, clever mechanics and the grand scope of the adventure proved to me that it deserves all the praise it gets.
Metal Gear Solid blew me away as a kid. The high production values, memorable cast, awesome boss fights and rollercoaster of a story was unlike anything I'd ever played and sparked my love for the series.
Picking the better game is no easy task and might come down to mere personal preference. OoT might be the more complete game however. If you skipped every cutscene in MGS, you could beat the game in just a couple of hours, really. OoT could devour 50-55 hours of your life. I'm not saying being longer automatically makes it better, but it is worth noting. MGS might have the better boss fights; the Psycho Mantis fight alone is better than all of OoT in terms of being memorable and in originality. Though having played them both in recent years, OoT may have aged just a tad better in terms of gameplay. But style and overall atmosphere of MGS is a bit more alluring than Zelda. Decisions, decisions.
I'm truly torn, but I'll lean towards Metal Gear Solid. I've got a soft spot for it, and honestly if I was presented right now with a choice to play both, I'd probably go for Metal Gear. The stylish espionage and crazy story edge's out Ocarina's more relatively standard "save the world from evil" plot. Both games deserve to go far though.