I've had a similar irritating noise on two bikes. On my Cannondale mech bike is was a slightly loose headset. It had passed the usual 'set the front brake and push the bike' test but I was able to confirm this by riding hands free. Tightening the headset just a bit solved this one.
On my ebike it was one pedal. I confirmed this as the noise stopped each time I stopped pedaling. It could have been something more serious, but it wasn't! One pedal needed lube. I disassembled both pedals and found one to have dry bearings. Another odd problem solved.
Silence is golden! I hate noises like that, and have found myself chasing my tail to find them more than once! I have found the loose pedal issue, loose crank arm, loose seat post, and the last one turned out to be the damned seat itself! I found that by leaning on the bike while checking other "stuff". It made a sound similar to a "click" I was hearing, and it dawned on me that the seat might actually be making the mechanical clicking noise I heard with every down stroke of my right leg. The "click" I thought I was hearing turned out to be a "squeak" coming from the seat! -Al