The funny thing here is that before he was outed by his former employers, Snowden himself was serving as an anonymous source. To now try and imply that using anonymous sources is somehow suspect when another publication does it is laughable. The suggestion that the Independent is working in cahoots with the UK government to discredit Greenwald falls under the category of a smear.
As has been noted, they say that the information comes from Snowden documents, but they don’t say that Snowden handed them over himself. Wikileaks made news recently for putting out a gigantic encrypted file for “safety” purposes. At around the same time, Greenwald’s significant other was exchanging Snowden documents with the person making an Assange approved documentary. It stands to reason that the events are connected. Given the recent turmoil in Wikileaks circles (specifically, the party meltdown in Australia), my personal suspicion is that the encryption key to that file dump was leaked to the Independent by a disgruntled Wikileaks staffer.