The Macintosh operating system was referred to as “system” thorough version 7.5. Version 7.5.1 used “OS” in the startup splash screen, and the name formally acquired the “OS” with “Mac OS 7.6” as a response to the clone program. If writing about an older Mac, I’d use “system 7.0” or “OS 9.1” for example.
In this case, the operating system has expanded to run iPods, iPhones and the iPad. Consider that “The iTunes Music Store” became “iTunes” when Apple started selling movies, TV shows, audio books and so on.
In the App Store today I noticed that Apple is indeed using “iOS” to refer to older versions of the system; the iBooks page notes that the app works with “…iOS 3.2 or later.”
“iOS” it is then.
Update: John Gruber confirms that iOS 3.2, currently running on the iPad, is a separate fork from iOS 4. I always assumed that wasn’t the case.