If you paid attention to the movie they are being evicted from their neighborhood. OK, you all know that. But they reference it as the 'Goon Docks'. It's just the area of Astoria, Oregon where they live. Mouth mentions this clearly in the movie at the beginning before they go on their underground adventure treasure-seeking for One-Eyed Willy's rumored 'rich stuff'.
It's obvious the word means nothing other than a sland term for THEM to denote a local resident of the Goon Docks. And they did live right on the water, hence the 'Docks' part. But in any case, A Goonie is just a local from the Goon Dock neighbirhood of their town - Astoria.