The NSA talks about them in internal documents, that they have absolutely zero incentive to lie on, that Apple is a part of PRISM. Why would the NSA lie about that on an internal document.
Don't you think there would be documents saying "We tried to get Apple to cooperate, but they didn't. Until they do, these are the steps, techniques, and hacks we will use against their technology." I don't remember seeing any such documents.