I've never tried it, but apparently you can modify the file: Safari.app/Contents/Resources/Reader.html
From an Apple community support page:
Do a right-click on the application Safari and choose +Show Package Contents+. An new finder window will open. There is one folder in there named Contents. Contents includes several files and folders, navigate to see the content of the folder Resources until you find a file named Reader.html. This is the file you want to edit. Most probably you will not have the rights to do so. Depending on your choice of text editor, you are asked for a admin password when opening the file or when you try to save it. I use the nice TextWrangler from BareBones and it opens the file without asking (it will do so later in the process).
Now edit the CSS to your liking and save the file.
Open Safari and check out how it looks.
And one more thing: With the next update of Safari your changes in Reader.html will most likely be overwritten. So you might want to keep a version of Reader.html at another location outside the application package Safari to re-implement your changes.
As always, proceed with caution when modifying default applications and have backups of both any edited files as well as your important data.
