Let's see...

Atari has had one good console. 2600. Everything else has been pure meh.

Sega has had two good consoles. Genesis and Dreamcast. Everything else has been meh.

MS has had one off the shelf pc and a defect rigged console. meh.

Sony has had two defect rigged consoles and one that is just too much for mainstream users for the first half of its life, though a really good system.

Nintendo has had 0 defect ridden consoles, 1 massive crapfest known as the virtual boy, 1 meh console (gamecube) and 8 other great systems, 7 of which dominated their generations and defined gaming for years to come (only the N64 did not dominate).

Let's face it, Nintendo is portable gaming. PSP, (the only true handheld rival Nintendo has ever had), is more of a music/video type of machine. Its software sales prove that.

Nintendo home consoles have done more to define console gaming than anyone else, from their controllers to their software, Nintendo has defined this industry.

Though I would give credit to MS for bringing consoles online and Sony for the first massive influx of "non-gamers" with the PS1.

In the end the 'best' gaming company has been and will be Nintendo.

I always enjoyed games, but when Dreamcast came out, I was blown away.
The graphics were awesome and games played so differently than other consoles.
Dreamcast wins for me.

Nintendo is the best hands down. See Superchunk and Final-Fan for reasons. They pretty much said it all.

After Nintendo, I would say Sony, Sega, Microsoft, and finally Atari.

1. Sony.
Never had DRE and they only upped my respect with the beast that is the PS3 (I've always loved cutting-edge tech)
2. Nintendo.
Only one knock and that is too many casual/mario games for my taste. other than that, no problems here
3. Sega
Never knew them (I started console gaming in '05) but I admire their resiliency/powerful consoles.
4. Atari
Let's face it. The 2600 practically made video gaming a viable industry all by itself. Too bad all their other consoles sucked.
5. Microsoft
The first box wasn't too bad, but had no games. (though you can't really blame M$ for that) However, the 360 just, well, sucks imo. Forcing the new gen early, RRoD... This just made me hate them even more than I already did for Vista....