http://www.nytimes.com/2010/11/11/books/11list.html
This article does say that the NYT will include online retailers which they exclude for the print book list. They also say that they will have to calculate the figures differently than they do their other list to account for the differences and manipulation attempts.
When you think of it ... it is no easy task. Some ebooks perhaps Ms Hocking's are 99c and available worldwide while most others are only to US. One book has 6 billion potential customers and the other 320 million. That has to be accounted for somehow. Then there is the old lower the price to 99c to generate sales and reviews then raise it to $9.99 to rake in the dough trick.
http://www.nytimes.com/2010/01/23/books/23kindle.html