It's hard to come up with the best, obviously, and sometimes I give credit to games that do something so exceptionally well but might miss the mark in other areas.
Grand Theft Auto: San Andreas is up there for me, and there's a reason ... it's basically a mishmash of other similar stories from Boyz in Da Hood and Menace 2 Society. The writing is great, the voice acting is among the best of any game ever, the cast is amazing, and because the core story doesn't stray far from its inspiration -- movies -- it ends up being much better than most other videogame stories that try to get original and are ultimately let downs. Criticism of GTA:SA and other Rockstar games from that era is that "the story goes off the rails," but if you keep to the core narrative, not the sub-missions and side-missions (CJ working for the FBI, CJ owning a casino, CJ infiltrating a CIA blacksite to steal a hovercraft and harriet jet...), then you have this core narrative around 4-5 characters, the police, and gangs/drugs in L.A. in the early 90s, and it's a story that just works. I think the criticism of "well those are part of the game so you can't ignore them..." are valid and it's probably just a mental exercise I make willfully ignoring them and sticking to the core narrative... I kind of dismiss those as "gamified" elements of the game.
"Crooked cops frame Carl 'CJ' Johnson for a murder that they committed in order to perpetuate institutional racism, gang violence, and police power in 90s Los Angeles. While trying to discover who really murdered his mother, CJ must upend this crooked cartel, find out who his real friends are, and discover his place in the world."
It's a simple story told well, there are a few twists, the bad guy is the best bad guy in any videogame ever, and it has an almost entirely minority cast that works. 15 years after GTA:SA we're still having a "Ugh, why are there no minority leads in videogames?" and "ugh, another one-note female sidekick..." while GTA:SA did it better than every other game since 15 years ago.
I think that RDR2 has one of the best narratives of any game ever made, like it's a story that is told so fucking well, and it's also so unique for a videogame ... to have characters with realistic motivations that aren't around the core videogame tropes (Save the girl, save the world, save your dad, save your kid) is refreshing. It's challenging in action videogames that don't fall into those motivation tropes, and even GTA:SA falls into those tropes for the motivation of a lot of missions ("Gotta save Kendyl," "Gotta save my brother," "Gotta save my friend," "Gotta kill this gang banger" [save the world]...). RDR2 doesn't do that and most of the motivations of the characters are legitimate motivations that we all feel: being pulled into something by someone who is important to you but you don't really want to go along with it... And just when you think that RDR2 might go down an obvious path -- Arthur meets his old love, Arthur protects John/Abigail's child son, etc -- it doesn't. His lost love *stays* his lost love, they don't rekindle their relationship and his love doesn't become the motivation for him to be better or do good things or save the world... Arthur stays Arthur because that is who he is, and she stays who she is (this is a very minor spoiler). There's a lot of TV shows that do that, from The Office to The Wire, characters have flaws and can't work through them, but there's almost no videogames that do that. Red Dead Redemption 2 is a story about the death of the American west told through the character of Arthur Morgan, it's as much about the world as it is about Arthur himself. For Arthur, it's a redemption story, from beginning to end the question is: Can Arthur be redeemed? Telling a story like that without falling into videogame story tropes is really difficult, and Rockstar deserves credit.
There's other games that tell tighter, more well constructed stories -- Gone Home and Grim Fandango for instance -- but I'm kind of filtering my "best stories" to genres of videogames that traditionally tell bad or cliched stories. Most action games fall into tropes for motivation: Zombies are destroying the world, monsters are taking over the world, your love is being threatened, your child is being threatened, your father/mother needs protection. I think they do this because videogames have trouble creating motivations for the player that can also be motivations for the character. It's hard to make you -- the player -- care about a dear friend in a game because, as the player, you can't really understand why they're important to the character and to you. Games usually do this lazily: "He's your brother, you have to care about him," "She's your girlfriend, you have to care about her." But it's hard to make you care about characters who have no natural relationship to the player. I haven't played Last of Us 2 yet, but the reason why TLOU1 doesn't really chart for me is because the motivations are pure trope: Zombie apocalpyse, end of the world, save the world, save the child; like those are the plainest motivations for moving through a story in videogames. The acting and writing is great in the game, same with the character animations, but I ding it down because the tropes are too obvious, too weathered ... "Oh, another story where a regular guy has to save a child and save the world from the apocalypse." The most interesting aspects of TLOU are, unsurprisingly, those that involve Ellie's growth and development as a character, because that's a little less explored.