Which is correct as far as comma, quotation marks, & footnote? "John Doe",1 or "John Doe," 1 or "John Doe"1,
The editor above has pointed to the dilemma of answering this question effectively; however, please allow an additional comment on the use of quotation marks and commas. Regardless of whatever is going on in the phrase or sentence, the first choice of "John Doe", 1 will never be correct because commas NEVER go outside quotation marks.
And, another small point, but one that still matters: regarding the spelling of grammar, please note that the word ends in -ar, rather than -er as it is spelled in one of the tags to the question. This spelling has been left as it was for the example. Grammer is, however, the name brand of a tractor. It is not the study of the rules of a language. Thank you.
What you require is not quite clear from what you have given. What information does 'John Doe' represent? Is it the name of the author quoted or is it representative text that is being footnoted? If it represents the quotation itself, then the superscript number appears immediately outside the closing quotation mark ("..."1).
The comma placement– if any– may depend on the larger context, the structure of the sentence within which this notation appears, but I would guess that it would normally follow immediately on the superscript ("..."1,)
Let me for now just refer you to a web page on footnoting (below), and then if you have more specific questions, you can get back to us.