The consummately correct way to say it is “A as in Apple,” since the “A” is meant to represent only the first letter of the word “apple” and not “apple” itself in particular. But in loosely informal formal situations, nobody will really take issue with you if you say “A for Apple” instead; only old-school schoolmarms would insist on the scrupulously grammatical usage.
In a call-center conversation, though, you’ll never know in advance who’s at the other end of the line; he or she might be a stickler for good grammar who's just waiting to pounce on the slightest grammar error on your part, and you don’t really want the call to be unduly prolonged by that. This being the case, stick to “A as in Apple” as a matter of long-term survival.
