With the new "Reply" to "Comments" feature on Facebook, I've noticed that replies to comments are treated the same as comments. But I was wondering if there is anyway to distinguish the two?
Yes. You can query each comment object in the Graph API for the value of its parent field. If the comment in question is a reply, then the value of the parent field will be a reference to the parent comment. Otherwise, no value is returned.
Reference here: https://developers.facebook.com/docs/reference/api/Comment/