Very tough choice because the 90's made some huge strides in very little time and the industry kept evolving and innovating massively - imagine going from Doom to Half Life in just 5 years! The gulf between a 2019 game compared to a 2024 one now is almost nothing.
Metal Gear Solid is a very strong shout because it told an incredible story and had some unforgettable gameplay moments. There's also Half Life as mentioned, Resident Evil 2, FF7, Super Mario 64, GoldenEye, Age of Empires 2 and many more.
I'd probably give it to MGS overall as it pushed the PS1 to the max and also exposed Nintendo's mistake in using cartridges as even some of the sound files were bigger than an entire N64 game! Games going from 2D to 3D was big in those days and Mario 64 was also a significant leap.
I really miss huge innovations like that these days.