OK here's a more detailed answer, starting from the ship entrance.
- In the first room go to the far right and down the stairs.
- Go straight down into the middle room of the three at the bottom.
- Surf then Dive on the patch of water.
- Go left then up into the second underwater room.
- Go up to the surface.
- In each of the rooms here, watch for a sparkle when you enter the room. Go to where the sparkle was and press A as if you're picking up an item. You should get a key.
- The key will open another door and there are hidden keys in that room and so on. In the middle room at the top there should be three sparkles, but you can't get to them right there. Instead, go back and in the room on the right side, then go left and check where those three sparkles were.
I don't remember exactly but either one of the sparkles is the scanner, or it's simply in the last room you get the keys for. Then take it to Capt. Stern who is in a museum somewhere...