An iPhone backup file managed by iTunes is encrypted with a separate key, which can be stored in the OS X keychain. A paranoid user might opt not to do so. The OS X keychain could be accessed by compromising the security of OS X, depending on how much encryption the user opted for. It's entirely possible for a paranoid OS X user to make things difficult in a case like this, even for the FBI.

On the other hand, if the FBI had some lead time, all of the above could be circumvented without Apple's cooperation.