Canonically, John Hammond spared no expense.
SGI and Apple computers didn't provide the most bang for the buck, or even the most bang, but they sure did use up the most bucks. Other than high prices, and the target market that goes with it, they couldn't have been more different.
The SGI systems were 3D rendering beasts, with a significant portion of their hardware dedicated to the task, making them fast machines for any task, because of the underlying capabilities needed to support that 3D hardware, and they were stable because of the robust Unix operating system. The Apple computers ran on commodity 68040 and an OS that couldn't preempt the software running on it, so a crashed application would take down the whole system.
A stock Amigo computer, at half the price of the Apple system, was just as capable, but supported better upgrades for live video processing. An IBM PS/2 computer running OS/2 would have had the stability of a Unix system, on lower-priced commodity hardware.
If they needed the 3D capabilities of the SGI systems, that was the only option, but if they otherwise only wanted to mess around with video, Amiga computers would have been better than the Apple ones, at a lower price. If they needed something robust, where a user process couldn't crash the system, other Unix workstations would have worked just as well, at a lower price, and an OS/2 workstation would have also worked, at a much, much lower price. Also, there's a rational to having a video-capable Amiga computer along with a robust network-focused Unix or OS/2 workstation, but if you already have an SGI workstation at your desk, you wouldn't really need another computer.
The computers make more sense for someone making movies than someone running an elaborate zoo, but considering how often characters in Michael Crichton's books are authors themselves, it makes sense that characters in his movies to have an affinity toward making movies, and buying the computers that would be used to do so.
Wasn't the Amiga essentially limited to interlaced video? That basically relegated it to a machine for games or realtime NTSC/PAL video effects.
Also I was never a big Amiga guy so I'm not sure, did they have an equivalent to QuickTime and Cinepak in 1992 to play video clips? Microsoft hadn't released Video for Windows yet.
Interesting though in retrospect they chose good platforms, Mac and UNIX are still around and flourishing and OS/2 died a death, although would a lot of OS/2 stuff have run on Windows?
Hammond spared no expense except when it came to Nedry, which was a critical mistake.
And the out-of-universe explanation is that the Jurassic Park production team had access to SGI "3D rendering beasts" because they needed to render some CGI dinosaurs. So these are both what they had to hand, and what the producers associated with powerful computers.