In first and second gear the power comes in the input shaft, goes down to the cluster and then back up to either first or second gear, which ever one is coupled to the main shaft and cluster at the time and then out the output shaft. In third gear, the input shaft and output shafts are locked together by the third gear synchronizer, so the power goes straight in through the input and out the output shaft. It's like one solid shaft in third gear. The cluster gear is still being turned by the input shaft but since the cluster gear is only turning gears not driving the main shaft there is no load on any of the gears, so they are quiet. No power is being directed though the cluster or first and second gears. Being quiet in third gear tells you that most likely the cluster, first or second gear broke a tooth. Especially if this noise just abruptly started. If it was a clunking U-joint, it would probably be noisy in all gears. You can take it further and say that if it was only noisy in second gear and not in first than either second gear or the cluster gear that drives second gear broke. Same for first gear. But if its noisy in both first and second gear than possibly the cluster broke at the front where it's driven by the input shaft or the input shaft tenth that drive the cluster broke. I'd drain it and see if any teeth come out.
Here is good video of a 4-speed that shows the power flow so you can visualize it. Same basic concept as your 3-speed. Choose which gears are noisy and then which gears they share in common that would be under a load. That might not be your problem but it's where I would start.
https://www.youtube.com/watch?v=K2IfBlea9cc