I realize this is an older thread but i have similar problems..
I have a 2014 and makes almost what sounds like a bearing noise. The truck only has 22000 on it and has had this noise since new. I'm told it's normal! But I must say it's irritating.
I've searched and seems there are a lot of Tacoma's with the same problems. It is semi intermittent when warm. I will be at a drive through where you can really hear it and it will sound off then slowly go away for a few seconds then start up again. Also, the knocking will speed up as you slowly give it throttle and rpm's. I still am under warranty with the drive-train, but no one seems to want to figure it out. I am planning (one more time) to take it to a different dealership. If I find anything out, I'll let you know.