ILM used Maya on SGI workstations throughout the 1990's and at least up until around 2003. They used Macs for almost every other computing aspect though, and most people had both systems at their desks. It should be noted that at one point places like ILM didn't need both SGIs and Macs because there were versions of things like Photoshop, Illustrator, Premiere, Framemaker and Acrobat for IRIX (I have copies of most of those on my SGIs). The problem was that they became antiquated quite fast after they stopped being made for the platform (the last version of Photoshop for IRIX was 3.0.1) and they needed the other tools handy. Maya wasn't the only tool that they were using their SGIs for though... Pixar's Renderman, Shake and a bunch of great effects software by Discreet (which is now Autodesk) were all great reasons to stay with SGIs.
On the question of what Pixar used... they are a software company (they develop and sell Renderman). But they try to stay platform neutral... more importantly, since they used their movies to help sell software, they have attempted to use a different platform for each major movie since Toy Story
(which was done using SGI workstations and a Sun Microsystems render farm). As I recall, Finding Nemo
was done on IBM workstations running Linux. Renderman has been available for many platforms, but only NEXTSTEP/OPENSTEP had elements of the software built into the operating system.
I'm sure that Pixar uses Final Cut Pro Studio, Logic Studio and Shake on Macs for some aspects of editing, but unless Disney has put an end to the software side of Pixar, they tend to like to make the point that their software makes great 3D renderings no matter what platform you are using. The only time a platform was given special treatment was for NeXT, but all the Renderman aspects of NEXTSTEP/OPENSTEP were removed when Apple started development on Mac OS X. Pixar gave Apple no special treatment after Apple acquired NeXT in December of 1996.