Possibility 1: Noise is coming from a uneven spacing from left to right side in the triple clamps. Double check the torque on the lower triple clamp.. then loosen the top triple pinch bolts and re-torque. The torque ain't much.. like 44 for the lowers and like 14 or 25 for the upper. Check your manual of course.
Possibility 2: Something above the valve body is broken or bent or hanging up. I recommend removing the forks completely from the bike.. but, you can remove the handle bars.. leave all the controls attached and lay forward onto a towel over the gauges or back onto tank.. pad it real well. Do only one side at a time unless you can lift the front of the bike by the frame or from the lower steering stem with an appropriate stand. Back off all the pre-load if so equipped, remove the cap, & again.. one side at a time
here unless the front suspension is unloaded. You can then fish out the spacers/washers and even the spring with a magnet on a stick. Inspect it all. If the clunk is at the top.. that is above the spring .. then it will be obvious.. there will be wear marks or some physical damage to the washers or spacers etc. You might even find a busted spring or the rebound adjustment shaft/screw if they are 2004 or later forks. Inspect everything thoroughly.
Possibility 3: the stanchion tube bushings are worn out. They would allow the fork tubes to knock side to side, front to back and up and down if they are pretty worn. This is a completely plausible possibility. I had to replace the bushings in the forks I rebuilt... too many wheelies and hard landings will do that trick. I imagine high miles, rough roads, bad seals, contaminants such as water, dirt and so on would lead to this. Forks have to come off bike and come completely apart to change. The good news you will be getting new seals and oil... and the bushings are really cheap if I remember right.
Possibility 4: Unlikely, but the screws that hold the valve body down in the fork case could have come loose. Seems it would be leaking all over if that was the case tho. You will have to remove the front wheel.. actually need the axle out of the way to gain access to those screw heads. They are internal Allen head.. 6mm I think. Again.. its very doubtful these would be loose without a shit load of oil pissing all over.
Possibility 5: Something is busted in the valve bodies. Good luck there. I don't know how the noise would even resonate up and out for you to be able to hear a clunk sound... but could be the case I guess?
Honestly, it's hard, if not near impossible, to diagnose this without seeing & touching it. If it is in the forks they are a fairly straight forward component and easy enough to tear into and replace the parts that are the culprit. I tore some 03 and 04 forks apart side by side once and took pics. I laid the parts all out, so you can tell what goes where in what order. Refer to this POST
for these pics. I never claim to do "how to" write ups and this is no exception. I assume you have basic mechanical skills and tools and more importantly know when you are in over your head. I know when I am in over my head and seek an expert when necessary. That said, if you have basic mechanical skills, the correct tools and a little patience you can easily tear into your forks for repairs and upgrades.