I was recently reading JJ Schachter's article "Facing the Truths of History" [http://www.yutorah.org/_shiurim/TU8_Schachter.pdf] and mention several episodes, such as the succession of the Brisker Rav to his father's position as Rav of Brisk and the Holocaust story of the 93 Bais Yaackov girls in Cracow. Does anyone have more information about these stories??

http://onthemainline.blogspot.com/search?q=cracow

That was concise.

It brings the NYT article but not the reasons for doubting the story.

For that you need to read R. Schacter's article.

However, see these arguments contra:

http://thumbsnap.com/v/rDxKYq1d.jpg

In addition, read the comments of that blog post.

The bottom line is that the story is a phantom, and the "Chaje Feldman" of the story cannot be shown to have existed, although there is a letter signed by someone calling themselves Chaje Feldman, detailing this story, and that letter seems to have been what sparked the knowledge of the story itself. There is simply no evidence that it occurred, and some good reasons to doubt it apart from the lack of any evidence - but by the same token, it also may have occurred despite these problems.