Teach Yourself Turkish uses this phrase ın a dialog as a equivalent to "Whats going on".  But two different native speakers have told me that don´t know what I mean. (Neither is from Istanbul).   Is this an "Istanbulla" phrase? 

Yes, it means "what´s going on?" or "what´s up?". No, it´s not an "Istanbul" phrase, any native speaker would understand it.

 I have heard Ne Var Ne Yok? in all parts of the country for many years.

Maybe we need to clarify the context. It´s used for a casual enquiry, like "How are things?" "What´s new?" "What´s happening with you". It is this sense of "What´s going on?"

Not, "what is happening?" with a note of panic in the voice, which would be "neler oluyor!"

I´ve said it to people and they´ve replied ´iyilik´ so I think they understood.

"Ne var ne yok" is the alternative of "Naber" in Turkish, so it is maybe translated in English like "What is up"...

Herkese teşekkürler.