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.