Do I need to be acting PIC when doing takeoffs and landings for my 90-day currency?
The regulation does not address whether or not you have to be PIC to establish currency.  It instead states that you have to do "three takeoffs and three landings as the sole manipulator of the controls" and in the "same category, class, and type (if a type rating is required)":


  Except as provided in paragraph (e) of this section, no person may act
  as a pilot in command of an aircraft carrying passengers or of an
  aircraft certificated for more than one pilot flight crewmember unless
  that person has made at least three takeoffs and three landings within
  the preceding 90 days, and -
  
  (i) The person acted as the sole manipulator of the flight controls;
  and
  
  (ii) The required takeoffs and landings were performed in an aircraft
  of the same category, class, and type (if a type rating is required),
  and, if the aircraft to be flown is an airplane with a tailwheel, the
  takeoffs and landings must have been made to a full stop in an
  airplane with a tailwheel.