I have this same issue (MacBook Pro Retina 15 2014, Sierra 10.12.3, Bose noise cancelling headphones).
It seems to play ok sometimes but more often than not it stutters so badly that is unlistenable.
Nothing so far has worked: reboot, pram zap, bluetooth reset (option+shift menu), disconnect/reconnect etc.
Curiously I thought I'd share what seems to work. I open the bluetooth system preferences and leave the window open. While the window is open the stuttering stops completely. Open another system pref and it starts up again.
I know it's completely daft to leave the window open - but I can live with that if it 'cures' the problem.
I'm sure with this info Apple should be able to find out what is cutting in and causing the stuttering.