Hi!
I have the same problem here. Got a new Macbook Pro 15" 2016, max specs, no bootcamp used and pop sound coming from the speakers (?) from time to time. To be precise, I feel like the "sound" is coming from the top central part of the body, like right under the centre of the touch bar. Maybe it's just my impression, can't say.
Here's a video I recorded close to the screen:
I spoke with a Genius last week and he had no idea about this issue. So we did a few tests and we ran the Apple Diagnostics, but the system was ok. He suggested me to format the hard drive and reinstall Mac Os Sierra and all the software from the scratch. And so I did, but it didn't solve the problem.
Also, I've noticed the pop sound in recovery mode and during the boot.
So I'd definitely say this is not a software problem.