Hi Jay,
First off, you're better of calling it an "eBook Reader". "eReader" is the name of a specific eBook file format, and it can cause great confusion to use it as a device name too.
If PDFs are vital to you (and I'm sure I don't need to tell you that they are a terrible choice for an eBook format!) then really your best choice by far is the iRex iLiad. It has an 8" screen and handles PDFs far, far better than any of the 6" screen devices do.
The Sony Reader and the CyBook Gen3 will both display PDFs natively; the Kindle requires them to be converted, as I'm sure you know. Conversion does not always work well.
The main benefit of the Kindle is access to Amazon's large range of books, of course, but the Kindle is only available in the US. The iLiad and Gen3 will both read MobiPocket books, which is the most popular format is terms of the number of eBook stores to choose from. The Kindle will read DRM-free MobiPocket books too. The Kindle, Gen3, and iLiad all support dictionary lookup (extremely useful!); the Sony doesn't. The Gen3 is unique in allowing you to load whatever fonts you wish onto the machine.
There's really no "best" choice. You have to decide what your priorities are and choose accordingly.
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