I find it very odd to not put the Nintendo EAD studios at #1 simply because their quality output is just insane. Every year theres at least two or three games that company puts out that's GOTY material. Just this last year they released Super Mario Bros. U, New Super Mario Bros. 2, Nintendo Land, and Animal Crossing: New Leaf. They are one of the incredibly few, if only, companies that have maintained the traditional mega-90s quality output of yesteryears. Probably because they have no other choice.
Valve, well if this is OVERALL, then yes. I can imagine putting them at #1. Team Fortress 2, Left 4 Dead, Portal, CounterStrike, and of course Half-Life. Though over Nintendo EAD? Thats a tough call being that the latter regularly revolutionizes the industry through its games. And recently what was their last "HOLY SHIT!" game? DOTA2 is in beta and has been for some time. CounterStrike: Global Offensive was great, but its the same old same old made exclusively for its narrow fanbase who I blame entirely for the series stagnate. Its kind of like when a new addition of a niche shoot-em-up comes out. I mean yeah its great but I've played this game a million times already. Before that was...Portal II? The company has clearly been busy and most likely with the overhaul Steam has been getting and the Steambox project.
#2 is a joke quite frankly. How the hell does developing one single game get you at that spot? I admit that I've never played Minecraft but I can't imagine a single game a developer could make and have them catapult all the way into that spot. Just switch Minecraft with Grand Theft Auto III, Ocarina of Time, The Sims, Chrono Trigger, Half-Life 1/2. It doesn't make any sense, and historically this is too early to call as there have been many example of developers making one hit wonders to then just be faded into obscurity with mediocre follow ups.