I went to a major retrospective of his at the Birmingham Museum and Art Gallery in October 2010. Each of the shots (including Afghan Girl") was labelled and K64 was definitely used. I am also pretty certain it was a Nikon as I've seen various references to his shooting Nikon whilst in Afghanistan on assignment in the mid-80s.
The shot was taken in 1984 and appeared on the front of Nat Geo in 1985. Therefore, as the last professional quality Nikon made before the end of 1994 was the FM2 series (1982 - 2000) it could have been an FM2 or possibly an FM2n as the "n" version was introduced in 1984. However, unless he was shooting an assignment with the very latest gear - probably a bit risky until it was proven - my guess is that it will probably have been shot using an F2 or an F3.
If you haven't seen it already, there's some incredible photography of his on:
http://stevemccurry.com/http://stevemccurry.com/blog