When I lived in upstate NY several years ago, I was close to a lake that boomed quite regular. Sometimes pretty loud. The explanation I was given was gas releasing from the lake bottom caused the noise when it broke the surface. The lake lies between two high ridges that sort of amplified the sound. It's a big lake, close on to 40 miles long and pretty wide, and old Indian legends had the noise as the "Voice of the Gods", and kept them pretty much away from the lake.