Should I give time to user to clear it's question by commenting on it?
You should do both ASAP, without waiting. Comment and flag. That way if they don't improve their question it gets closed (since it's unanswerable and even if someone answers when OP edit it may invalidate answers it may have) and if they do improve the close voters will vote to leave open (if they aren't rubber stamping :/) or if he edits in the first 5 days of being closed it will get in the reopen review queue. That's The Right Way™.