Hello Sebastian,
if you stay in Flushing,you will easily find best locations. For those ships heading to/from Steenbank Pilot, the place where they come closest is near the so called "Gevangentoren" or at the "Windorgel" little more outside, but you can well take them at the complete Boulevard/Beach section. The ships heading to/from Wandelaar Pilot, which is the majority, can be well taken at the entrance to the Marina/Pilot Boat Harbour or little inside at the entrance to the old harbour (Binnen-/Buitenhaven). Distances may depend on how the ships moving during the pilot change. You will have the sun opposite during the noon hours.
Flushing East ports are closed to public,however good pictures can be taken at the entrance to the port,on the Western side of entrance you will find public access.
Enjoy
Rgds Niko