gohawks

Second answer from online Toyota mechanic

"This used to be a very common issue with the 3VZN engine, the noise is coming from the front main bearing, the bearing has a little too much clearance which causes the low pitched thumping type noise, my own 4-Runner did the same thing and I actually drove it for a long time but the noise became annoying so I finally replaced the bearings.
The main bearings have numbers that indicate the clearance between the bearing and the crankshaft journal, they are numbered from #1-5, the solution is to replace all the rod and main bearings and reduce the clearance of the front bearing by installing a #5 bearing,all of the other bearing numbers should stay the same, using a different oil viscosity won't be of much help.
To verify the condition of the bearings as I have described, remove all of the drive belts and see if the noise goes away. Doing so will remove pressure from the front pulley and lessen the noise, a lot of times there were complaints by customers of this noise after a timing belt was replaced, the new timing belt and the tighter drive belt adjustment would cause this noise occur.
I have never experienced an oil pump causing a knocking noise. "

motoracer47

i believe this is good advice. i think there has been alot so far in this thread. remove the drive belts and see if it goes away. the thing with bearsings, is there are a couple of different ways they can wear and cause noise. could be a main(front)like the online mechanic is saying, causing slight movement of the crank, creating a rattling noise. could be a rod bearing wearing, allowing slight up and down movement of the rod against the crank, almost same noise. every now and then you can get thrust clearance problems on bearings as well, however for the mains this is usually at the rear, and because of high force presure plate springs on manual trannys. i believe rod bearings can also have thrust issues, causing it to twist slighly on the journals, may not be describing that one correct. i too have never heard of an oil pump causing knocking noises, but could be. you might want to buy a stethoscope so you can listen yourself, they are cheap at harbor frieght or northerntools. with that, it should be fairly easy to tell if its coming from the pump, or somewhere else along the block. if you take off the upper timing cover, you should have room to stick the stethoscope down and touch the top of the oil pump. here is a pick of the front of the motor with covers removed, pumps at the bottom. btw, if you do change the belt and oil pump, might as well change the water pump while your at it.

in this pic, the water pump is the aluminum cover with pulley on the driver side of the belt, between the cam and crank pulleys. the oil pump is the very bottom piece, and the crank snout go through it. you should be able to stick the stethoscope rod down between the timing belt pulleys, almost like you are trying to touch the crank pulley, but just above. if you can hear the sound loudest there, then it very well could be the pump, or the front main. but if its the pump, should be very obvious when using the stethoscope.