The NRC rankings came out in 2010, but they collected the data in 2005-2006.
It literally took a team of people about 5 years and $4 million to create the ranking, yet they were still not completely satisfied with the result.
I have attached a summary article so you can draw your own conclusions, but I am of the opinion that a single, definitive ranking is neither possible nor interesting - even at the department level, never mind at the university level.
I do find the NRC database useful though (as long as it is used with care, due to its age) and I like the concept of the user interface program that Phds.org provides. The interface gives the user the ability to change the weighting scheme to match their own priorities as well as probe the database and perform sensitivity analyses. It would be nice to have such an interface for the CDC database.
Here are some examples of good, specialized Phd programs that are not widely known outside of Massachusetts that are revealed by the high level of granularity of the NRC database.
Clark is a really tiny university (better thought of as a LAC with a small number of small Phd programs), but a world class geography program that few know about.
http://phds.org/rankings/geography
Tufts is a small university that has a world class nutrition program that few know about, because it is traditionally aggregated with agricultural sciences rather than health/life sciences.
http://phds.org/rankings/nutrition