Reference-style in the cover letter for resubmission of a manuscript
In my opinion, what you really need to worry about here is clarity.  Cover letters do not generally have a prescribed style, so you can probably pick whatever style is most clear in place---that will not be a number pointing to a different section or document.  

Personally, I'd probably not do any formal citation at all, but instead just reference the work in prose, e.g., 


  I developed and strengthened my criticism of XYZ's 2010 paper in the following way..."