You can also change the iOS Reader.html CSS on iPad, iPhone or iPod, confirmed working on iOS 8.1.2 iPad Air 2. Here's how:
You will need to Jailbreak your iOS device, and download a file system managing app called iFile. Then you'll have full Explorer/Finder functionality on your iOS device.
Next, navigate to the folder:
This is the location on my iPad Air 2 with iOS 8.1.2, it may differ for you. If you upgrade to the paid version of iFile for $4, you can do a search system wide for the Reader.html file, which is what I did.
Open in Text Viewer, now just change the CSS as desired, anywhere you see the "font: -apple-system-*" declaration.
If you want to change the main body typography, add a font-family declaration to the .page tag. For example:
You can do the same thing to edit the page heading under the h1.title tag
Save Reader.html, reload the Safari webpage, and enjoy your new Reader font!