AppleScript Save As Dialog in Safari Reader Save As PDF
Here's how you'd do this:


Go into the finder, and drag whichever folder you want to use for this into the "Favorites" section in the sidebar (enable the sidebar in the view menu if it isn't showing).
Run this script, but replace menu item "Xcode" of click menu item "Xcode" of menu 1 of pop up button "Where:" with the name of the folder you added to your favorites.

tell application "System Events"
    tell application process "Safari"
        set frontmost to true
        tell menu bar 1
            click menu item "Show Reader" of menu "View" of menu bar item "View"
            click menu item "Save As…" of menu "File" of menu bar item "File"
        end tell
        tell window 1
            repeat until sheet 1 exists
            end repeat
            tell sheet 1
                click pop up button "Where:"
                repeat until menu 1 of pop up button "Where:" exists
                end repeat
                click menu item "Xcode" of menu 1 of pop up button "Where:"
                click button "Save"
            end tell
        end tell
    end tell
end tell