In short
Simple. City bus 13 links the Souda quay to Chania (Agora terminus) in ~20 min for ~€1.80 pre-bought, every 30-60 min, 7 days a week. Alternative: the KTEL Rethymno-Chania bus via Souda. The Piraeus ferry arrives around 05:30-06:00, just as line 13 starts.