As I mentioned before if the clause is extra and we don't need it, it's put in commas. If the clause gives us information that we need, there are no commas. Here maybe there's more than one person who is called James, so we need the information (who was waiting for me) to know which James we mean.
Good luck
No, it's not good English to write, "Where is James who was waiting for me?" The sentence is not good whether it has a comma or not.
In any case, the issue of a comma is unlikely to be relevant since this is surely a spoken sentence.
In my dialect, the following are possible:
"Where is this James who was waiting for me."
"There was someone called James waiting for me. Where is he?"
"Where is James, the man who was waiting for me."
