Without participating in the Apple Made for iPhone (MFi) program, your options are truly WiFi or Bluetooth LE. Wi-Fi is more hungry, and if you are not very careful in choosing chips, it will be difficult to implement them. Bluetooth LE is only supported on the iPhone 4S and the new iPad (i.e. 3rd-gen); it will probably be supported in future iOS devices, such as the new iPhone and the little-known βminiβ iPad.
Just Bluetooth 4.0 is not enough, in my opinion, it should be Bluetooth 4.0 LE (low-energy option). Support for such devices is provided in the iOS 5.0 SDK, and then using the CoreBluetooth framework. See Apple documentation for CoreBluetooth [free developer registration required].
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