According to the Bible, Jesus was crucified in a place known as Golgotha or Calvary (both names translate to "hill of skulls") outside the city of Jerusalem.
I would go with the Pasig River.
Manila (not "metro Manila") is located at the mouth of the Pasig River. The Marikina river is a tributary of the Pasig river and flows through Eastern "metro Manila".
Please note that Manila and Metro Manila are not the same. Metro Manila describes the huge conurbation that also includes the much larger Quezon City and also other areas. The river that goes through Manila itself is the Pasig River.