Personally, i thought Rockstar Games did well- GTA IV, Midnight Club Los Angeles, Red Dead Redemption, LA Noire, Max payne 3, GTA V. All very good.

Mentions to 2K, Epic Games, Naughty Dog and Media Molecule too

Ad hoc development team
=)

Square Enix 1st Production Department

Naughty Dog. They didn't make one bad game this gen, they brought survival horror back from the brink of moronosity, and took action/adventure to a new level.

Honorable mention to 2K Games because of the NBA 2K franchise killing NBA Live.

Naughty Dog dominated this generation and has been setting standards since Uncharted 2, so thats about....what... four years now? They haven't relinquished the title yet, either. Honorable mention goes to Bioware.

The best publishers of the gen have to be Ubisoft, Sony and then Nintendo.

Valve.

Portal 1 & 2; L4D 1 & 2; TF2.  No-one else has come close.  I don't actually think they've put a foot wrong this generation (if we count the generation from ~2007-2013)

Special mentions:

Naughty Dog:  But I haven't played The Last of Us yet so it's still a while until I'd nominate them for the top spot.

Nintendo EAD Tokyo:  I don't know whether this is actually two separate studios, but whoever it was who made Mario Galaxy 1 & 2.

And just a few more I'd like to bring up:

Insomniac Games:  It feels weird listing them considering they disappointed me hugely in the past 3 years (All 4 One; Full Frontal Assault; Fuse).  But that's ignoring the fact that they put out 3 excellent Ratchet games (Tools of Destruction; Quest For Booty; A Crack in Time).  And I had a lot of fun with Resistance 2's co-op mode & Resistance 3's single player too.

Gust Corporation:  This might just be because I'm playing Atelier Ayesha at the moment, but I feel like they've made 3 excellent JRPG's in a row now (Totori; Meruru & Ayesha).  I haven't played Rorona & Ar Tonelico Qoga yet though; which might sour of my opinion of them.

Studio Liverpool:  WipEout Pure; Pulse & HD Fury.  3 fantastic returns to form for my favourite videogame studio of all time.  And technically all part of the 7th gen.  But their output could've been a lot better, so they don't hold a candle to some of the other teams I've listed.

Atlus, Naughty Dog, Square Enix, Rockstar and some Nintendo studio.

In no particular order :

Valve - The sheer track record of titles, and the rapid growth and ultimate changing of the gaming landscape with Steam, definitely deserves it's place on here.

Naughty Dog - 4 games released this generation (3 AAA status and if the PS3 didn't get such bad rep early on, I imagine they would have had 4 AAA games.)

Media Molecule - There hasn't been a game that right out of the package that brought me as much anticipation, joy, freshness and just pure-hearted fun as Little Big Planet. You could feel the love and creativity that were put into the game and it was just plain a wonderful, fresh experience. This game exemplified why I bought a PS3 over 360 in the first place.

Santa Monica Studios - Collaborated on numerous highly under-rated games (Warhawk, Starhawk, Twisted Metal) as well as produced arguably the most graphically impressive game on any console in (God of War III). That's in addition to their work with (Flow, Flower, Journey, Unifinished Swan).

ThatGameCompany - Some of the best, artistic works I've ever witnessed. Flower is easily in my top 5 games of the generation.

Rockstar Studios - I'm not the largest fan of GTA in the world, but their stories are actually really pretty well written and sequenced. Midnight Club's are always highly underrated IMO however, their true gem though was Red Dead Redemption (One of the best games of the generation). Open world, fun and completely hit a home run for how open world games should be designed. (If only they could develop my dream of a Medieval open world game happen like Game of Thrones esque, I'd be very happy).

Activision/Blizzard - As much as I actually don't like Call of Duty. Hats off to them. They made easily the most successful game series (Call of Duty) on consoles and also pushed out (Starcraft II, Diablo, World of Warcraft expansions)

Nintendo - Wii Sports deserves a well placed spot after dominating the entire video game industry and literally carrying Nintendo to lofty heights (Almost single handed). Nintendo also ended up releasing great titles like Mario Galaxy, Smash Brothers. I still felt they left some games to be desired on the table, but they still released some killer applications like usual Nintendo.

From Software - Demon's Souls was a fresh spin on what has been somewhat of a dead genre for several years now and added a level of punishing challenge rarely seen on consoles nowadays.  Maybe it's my age, but I appreciate a throwback to how games used to be.

Honorable mention :

Bungie (Made iterative Halo, but certainly didn't re-invent the wheel lost a lot of ground to CoD),
Epic Games (Gears of War was an epic game, but subsequent sequels were lack luster and iterative),
Polyphony Digital (GT5 was a sight to behold but released very late and wasn't ready when it was released).
Bethesda - Also deserves credit here with several AAA titles.  I lose a little respect for them because I feel like their games are typically somewhat overrated and filled with quite a few bugs that other games wouldn't get the pass for having. 

Alright then, Nintendo (by that I mean EAD). They made the two highest rated games of the generation, after all.

I can't choose ND, because the Uncharted series got a bit same-y for me personally, and TLoU is great, but that's one game. And it's just released. Lets wait a few years to see if people remember it as fondly as the Galaxy games.

Irrational, Nintendo EAD Tokyo, Naughty Dog and Retro, in that order.

EDIT: Order switch :P