The New York Times article seems to be talking about the extra gain, which I presume means gain in addition to beating the benchmark. Here's the quote:

"Over the last 10 years, the return on those “public asset classes” has surpassed expectations by more than $2 billion, according to the comptroller’s analysis. But nearly all of that extra gain — about 97 percent — has been eaten up by management fees".

I read this as meaning that the extra gain meaning gain minus benchmark gain was $2B and most of it was eaten by fees (which is still bad, but not as bad as the article and its title seem to suggest).