In Martha's Vineyard there are eels that make an extremely loud clicking sound. We thought they were little crabs feasting on the bottom growth of the boat, until a 'local' told us what they were. They would be intermittent and not in every mooring spot. The live in the mud and are not in the Boston Harbor area. Understand you ruled out critters, but there may be all manner of local aquatic life that may be down there.