I'm doing a comparative review, since in many ways these games are far more similar to each other than you see outside the same series. They've both been trying to resurrect their troubled franchise with a lost on an island survival/exploration/stealth story, and they've been fairly popular for it.
Also one of these games does just about everything better than the other, so it's going to be a fun review.
Mild some spoilers ahead.
StoryLet's start with the story. Tomb Raider is classic reluctant hero(ine) story - it's quite well executed, but it's hard to get any more cliche than that. Far Cry 3 is descend into madness story under thin veil of reluctant hero - something like what Spec Ops: The Line did so superbly. The execution is probably far too subtle, and it's easy to miss half of what the game is trying to tell you during your first playthrough, especially since you have much freedom to do things in your way and order, so traditional story telling gets diluted, but not to the point where environment becomes the story itself like in Skyrim or Fallout: New Vegas. This is a close one, but I feel Far Cry 3 is doing a bit better.
As for protagonist, Jason is highly generic on purpose as demanded by the descend into madness genre - he must be an empty canvas, and any particularly distinct characteristics would overshadow the descend. Lara can be developed much more, since there are no storyline constraints, so on this point Tomb Raider has small edge.
For antagonist, Vass is a strong contended for top 10 bad guys of all times, and let's just say none of the Tomb Raider antagonists has any shot at that list. The biggest problem with Far Cry 3 is that it has too many antagonists who are not Vass, and they are just so much less exciting by contrast.
Likewise, the team of minor supporting characters in Far Cry 3 is far ahead of blandness what Tomb Raider has to offer. The contrast couldn't be more extreme - in Far Cry 3 everybody except protagonist is extremely interesting, and in Tomb Raider nobody except protagonist is.
And before we leave the storyline, let's talk about sex. Lara in her earlier incarnations was famously oversexualized - it feels weird why in retrospect, her body had fewer polygons than a half-decent rendering of a teapot - but they very successfully toned it down and it's no longer what the character is about. Interestingly while they pretty much had to completely desexualize Lara (not counting a couple borderline creepy cutscenes) to restore her position as a serious character, sex is used quite skilfully and with much better taste than you'd expect from a video game as an element of Far Cry 3's storyline, and then again in Far Cry 3: Blood Dragon.
ExplorationMajor part of both games is exploring the island you're trying to escape from.
The island - in Far Cry 3 you can actually explore wide open spaces on your own - the only thing stopping you is danger it represents, not artificial walls. In Tomb Raider you're largely constrained to following the storyline with just minor detours. Both are valid ways to design a game, but Far Cry 3 surely wins this.
Tombs and ruins - in Far Cry 3 you can explore the whole island looking for ruins - some are fairly easy, others are obscure and extremely rewarding when found. The problem is that you can just buy maps showing you locations of them all cheaply, and that kills a lot of fun. In Tomb Raider the titular tombs are just small detours from path of the main storyline, and it's really not much of an achievement that you found them. On the other hand, Tomb Raider executed platforming and puzzle aspect of tomb raiding far better than Far Cry 3, where the only really hard part is getting there, and once you're there they tend to be pretty straightforward.
Wildlife - at least during the first playthrough Far Cry 3's island is teeming with extremely dangerous wildlife in addition to more conventional human enemies. Then you learn some simple techniques for avoiding them all and the game loses a lot. Tomb Raider's island contains mostly highly scripted wildlife and doesn't feel alive at all.
Enemies - enemies in Far Cry 3 are highly dynamic and coordinated threat and you have countless ways to deal with them - paranoid avoidance being a good start early game. Even if you're really good at the game, you'll be frequently running away from unfavourable encounters, to strike back some other time. In Tomb Raider there's really not much sense of a threat, and the enemies are pretty dumb.
Graphics - the Far Cry series started from a tech demo, and is still unmatched in terms of amazing graphics - it's one of the reasons why the tropical island is so tempting to explore, and during some of the storyline missions the game far outdoes even that. Tomb Raider's graphics are merely decent - I feel they put far more effort into making Lara look (tastefully) good than into making the environment look good.
MechanicsOf everything I've mentioned so far, Far Cry 3 sounds like an amazing game, and Tomb Raider as still a very good one. Unfortunately when it comes to mechanics both games leave a lot to be desired - and for Tomb Raider a lot more than for Far Cry 3.
Quick time events - Far Cry 3 thankfully largely avoids them. For Tomb Raider they are everywhere - some storyline sequences require you to perform a combination of six or more quicktime events, including repeatedly bashing various buttons, and other such awfulness which is bad enough on a console controller, and completely unacceptable with a mouse and keyboard. This isn't just an inconvenience - endless quick time events after quick time events sap all the fun from this game. I strongly dislike QTE in any game, but I've never seen a game which relied on them so heavily as Tomb Raider, on any platform.
Skill Tree - neither game provides terribly many customization choices. Vanilla Far Cry 3 locks out most skills until you progress storyline, which is probably fine on your first playthrough, but most mods get rid of these limitations for a reason. Nothing exciting here in either game.
And everything elseMods - I'm a PC gamer, a game without mods is incomplete to me. Far Cry 3 has some limited modding scene - it's mostly balance and such minor tweaks, but that makes second and further playthroughs a lot more interesting. Tomb Raider modding scene looks completely nonexistent.
Franchise - both franchises needed a serious reboot. Far Cry 2 was a total disaster, and Tomb Raider series was in even worse spot. Far Cry series already got another amazing game in Far Cry 3: Blood Dragon, so far Tomb Raider series didn't get any major new content, but it definitely managed to turn Lara into a serious character. Hopefully the sequel Tomb Raider: No More Quick Time Events is coming soon.
And that's why Far Cry 3 is 9/10 totally amazing, and Tomb Raider: Quick Time Events is just a 6/10 almost good but no. (I could definitely imagine this game to go to 8/10 if some modder removed every single QTE from it, but without active modding scene I don't have much hope)