Without joining Apple's Made for iPhone (MFi) program, your choices are really WiFi or Bluetooth LE. WiFi is more power-hungry and, unless you're very careful in your chip selection, can be difficult to implement. Bluetooth LE is only supported by iPhone 4S and the new iPad (i.e. 3rd-gen); it's likely to be supported in future iOS devices, such as the new iPhone and much-rumoured 'mini' iPad.
Just Bluetooth 4.0 isn't enough, from my understanding, it needs to be Bluetooth 4.0 LE (the low-energy variant). Support for such devices is provided in the iOS 5.0 SDK and later with the CoreBluetooth
framework. See Apple's documentation on the CoreBluetooth
framework [free developer registration required].