Many times, the page number in pdf is different than the printed page number. How to make sure the other person doesn't get confused when we say "it's on Nth page".
If you're talking about the PDF of a paper published in an academic journal, then the answer is unambiguously: refer to the journal page numbers, i.e. the numbers at the bottom of each page. Those are the ones features in (almost all) citation styles.
Otherwise, if the document is a random PDF found on the web (not coming from a journal), just avoid referring to pages. If you absolutely must, refer to the page numbers printed on the paper, as it is the only thing that makes sense to someone who would print the document.
In informal communication like email I use a notation along the lines of "page X (PDF page Y)". By providing both numbers, it is easy for whoever is browsing the PDF to figure out if X or Y is referring to the internal page numbers or the PDF page, and then use whichever one they want to find the content.