Between the two of those; Bioshock. Zero doubt about it. Tomb Raider is dumb fun, and while it does deliver it's narrative well, the writing itself is as clichéd as you'd expect from the series. Bioshock on the other hand, is a terrific game that is mainly considered such due to it's superb story-telling.
While I think The Last of Us was excellent in every aspect, it isn't a particulary origin game by any means. Bioshock on the other hand goes out it's way to deliver a string of twists, one crazier than the other, and they actually manage to tie it all together at the end in a way that is both emotional and impressive.
A few other games I'd readily suggest are smaller titles that you may, or may not, have gotten the chance to play. "Amnesia: A Machine For Pigs" has the best writing I've seen in a long time, hands down."To The Moon", which was released last year, is a small indie game you'd be able to pick up for a small sum, that is basically an interactive novel, it's also impossible to forget.
Finally, they just released an Enhanced Edition of Baldur's Gate 2, which ranks up there as having one of the best stories in gaming, of all time. It's no Planescape Torment, but still..
Yet to play Gone Home and Brothers, myself, but I hear those are worth a look.