Do you feel it in the steering wheel? If so, it could be the intermediate steering shaft. Very common on Highlanders and other Toyota models from that time frame. The grease that lubricates the splines dries out and causes the telescoping shaft to catch instead of sliding smoothly. Supposedly it is just an annoyance and not a failure risk. You could replace the shaft if you want. There are various folks on YouTube who claim to be able to fix it temporarily by injecting oil past the rubber boot in the footwell using a hypodermic needle. Never tried that myself. I've just lived with it.

 

Yeah likely the worn intermediate shaft. Somewhere there is a Toyota OEM grease kit. I've seen them. Supposed to help

 

I would also go with ISS. If not that, then maybe the clock spring. I would also say the stabilizer links, but since you've replaced them it is unlikely to be bad.

If you do go with ISS, I would recommend getting the OEM part. They upgraded the ISS and so far nobody has reported issues with the redesign. It is easy to replace. I was able to access it through the front left wheel well, with the wheel taken off. Then contorting my body to get access to the bolt that is in the driver's foot area. Injecting grease into the old ISS is only a temporary solution and the clunk will return.