Why are the books I want $2 more than on Kindle? Guess I'll order through Kindle..
Amazon in general has equal or better prices than Apple for the equivalent merchandise. It really does not matter why. Just shop where you get the best value, selection, and convenience.
As Jim Z hints, Kindle books can run on a wide range of platforms, including iPads and Macs, by the use of the appropriate apps, which by the way are free.