Why are you only considering the Kindle and the Sony? The dominant eBook format out there is MobiPocket, in terms of number of devices which support it, and there are numerous Mobi bookstores.
Practically speaking, publishers generally release all eBooks in all the major formats; so in a sense it doesn't really matter. Yes, "numerically" the Kindle book store sells considerably more books but whether the "extra" ones are ones that the typical reader would ever want to buy is highly debateable.
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