Nah, even atari had one.  

And there were some arcade cabinets that had some form of motion control as well.

But people are kind of missing the point.  Innovation doesn't necessarily mean you were the first to ever do something.  Jimmi Hendrix didn't invent playing the guitar, but he was innovative because he did it in a new and unique way.  Henry Ford didn't invent the automobile, but he was innovative because he devised a way to produce them in an affordable and streamlined manner.  Even though the idea for motion controls existed for a while, that doesn't mean subsequent attempts at motion controls can't be innovative, provided that they offer a unique take on it.

As for the topic, it's really a no brainer.  Nintendo, and it's not really that close.  They've worked on many of the innovations we had in terms of control, they basically established handheld gaming as a thing, they came up with the first motion control solution that was useful beyond a handful of games and could actually be integrated into traditional games (Skyward Sword, Mario Galaxy), popularized (and maybe invented) rumble, the dpad, established touch screen gaming (not the first, but the first to actually work well and have strong software), and so on.  They had internet functionality on the NES and SNES, they had mouse peripherals, the balance board, Virtual boy, and we can keep going.

Beyond the hardware component, there are certain genres that really wouldn't exist, at least not in their current form, without Nintendo.  Donkey Kong and Super Mario Bros set the tone for platformers, Mario Kart basically invented the Kart racing subgenre, Mario Party established the board game style video games, Pokemon established the monster collecting thing (not the first, but the first to do it really well, and possibly the first to make trading a centerpiece), Mario 64 established what 3D platformers would be for the next decade or so, were possibly the first to do handheld/console integration (Pokemon Stadium), developed the Metroidvania (I don't really even get why the vania part gets included since Castlevania didn't add a whole lot to the formula) style of games, and so on.  Out of the three major developers it would be nearly impossible to argue that Nintendo's games have not been the most influential in the industry.

The only company that really comes close to Nintendo is Sega.  They had the first system that really did online well (albeit with 56k), system add ons, game add ons (sonic and knuckles which was really an early form of DLC), the VMU, and even had a broadband streaming game service back in the Genesis days.  The problem with Sega was that their innovations typically weren't as well thought out.  Great concepts, but often shoddy delivery.

I certainly won't deny that Zelda had a massive impact on console gaming or that the cartridge battery was much, much better than passwords (for developers that could afford it).  For two generations, it was very important.  I just don't want to see the influence of computer games to be discarded.  They could already save game progression and that model would eventually become the standard when CDs hit.

Also, going back to my first post, I just discovered that Nintendo was not the first with a handheld gaming device.

Not only it was cart based but it also featured early d-pad-like 4-way control using the 4 buttons.  Wow.  Not bad for 1979.

Oh yeah. All too often computer RPGs like Ultima are overlooked. I definitely want to give groundbreaking games like that all the credit in the world.

Obviously Sony. They created all the modern standards.

Nintendo > Microsoft > Sony

Nintendo saved the gaming industry and defined most of today's gaming patterns! :)

Microsoft defined console online gaming, introduced achievements and the headset jack on the controller was a pretty nice idea!

Sony saved us from Don Mattrick

Obviously Nintendo and by far.

I agree with this. Nintendo has the most innovation but not always the best. 

Nintendo. No contest.

Nintendo by a mile for gameplay followed by a bit for hardware.

Even though Sony is my favorite gaming company, i have to go with Nintendo.