I have a similar vehicle in my 99 ES300 and these cars are known for their clunking. First culprit is usually strut mounts, second is sway bar bushings. How are you sure the strut mounts are good? Have they been replaced recently? An easy way to check for the strut mounts (this confirmed it for me) is to spray silicone lubricant on the outside of the mount in between the rubber and the outer metal hole. Spray slowly and give time to trickle down. Repeat it numerous times. If the sound goes away it's your strut mounts. There's no other true way to check them other than pulling out the strut assembly itself. For the sway, or stabilizer, bar bushings, reach in and pull on the sway bar to check for any kind of give. If it moves at all then they need to be replaced. Even if there is no movement with your pull, sometimes they are still bad. They are fairly cheap anyways at 10 bucks or less per bushing, so it's good insurance to replace them anyways if they haven't, and it's cheap and easy troubleshooting.