Where can I find a graded reader with pinyin alongside the simplified characters?
If you don't mind, you might want Mandarin textbooks for lower grade elementary school used in China. 
And some storybooks also have Pinyin on every character.
You might search jd.com or taobao.com to find some examples using keywords like "识字 拼音", "小学 课本".

If you want get pinyin when reading on screen, you might try Lingoes Translator (offical website) with Chinese Dictionary installed.  This software can pick up the character under your cursor and perform a query automatically (and you get pinyin)(this may require an option to be enabled).