That article's author isn't very intelligent when it comes to photography. She assumes that using an iPhone means no skills are required. The truth is, skill is required because Latham (a photographer) knew the iPhone would be good enough, and found the right light to make it so.
Instagram is neither here nor there.
EDIT: Just found this from the photographer's blog:
Below is a set of images shot with my iPhone and processed through Instagram (I shot others with an ”actual” camera, but these are my selects from my iPhone set). Below are; Rodriguez, Ibanez, Teixiera, Jeter, Rivera, Chamberlain, Sabathia, Granderson and Gardner.
Bold emphasis mine. So yeah, it wasn't as if he only went in with an iPhone. The NYT simply chose that shot because they liked it. Editors are as quirky as regular consumers when it comes to picking favorites, and neither tends to care what equipment was used. The BI article is just a fluff piece.