Re: DC's New 52: Reviews and Discussion (Spoilers welcolme and likely)
Did Batman R.I.P. still happen? Because Bruce had his mask off right in front of the Joker during that. If that story still stands, then there should be no doubt whatsoever that the Joker knows who Batman, and by extension the rest of the family are.
"In blackest day, in brightest night, beware your fears made into light. Let those who try to stop what's right, burn like my power: Sinestro's might!"