iPhone seems to have a better selection of apps for pilots at the moment (this is likely to change as Android-based phones continue to dominate the market). That said I have found plenty of nice and free Android apps for stuff like weather, NOTAMs and flight planning.
Disregarding apps, Android phones, of which I've mostly used HTC's, are superior in pretty much every other aspect. I would recommend the HTC Desire HD. One important point against the iPhone for aviation use is that it is very temperature sensitive. It will overheat if exposed to direct sunlight for any prolonged period of time and the warranty does not cover use below zero degrees C. (There is at least one PPRUNe thread about this if you care to search)
As an additional argument against Apple, they have a history of extremely anti-consumerist behaviour which continues to this day. From banning any apps that are considered the tiniest bit controversial, to using special screws in their devices to keep independent repair shops or private individuals from performing repairs (replacing the battery in an iPhone4 is NOT straightforward compared to any HTC phone!) ... I would not buy anything with an Apple logo on it until this behaviour changes, if ever.