For me it was the axles on my 2012 6-speed. I had my mechanic swap the stock axles out for some Insane Shafts and it alleviated the issue, for the most part. My mechanic said that there is still a very slight vibration which I feel as well and it could be an internal transmission bearing issue or the half shaft. He recommended leaving it as-is unless it gets worse.
I highly recommend Andy Yang at SoCal motorworks if you happen to be in the Orange County area. Insane Shafts is also local here and can give you a cash deal on axles. 7k miles on the new axles and they feel fine, OEM is pretty pricey and I've heard some not so great things about the no name 3rd party axles out there.
Hope this helps!