Which has better sound output -- an iPhone 6s or an iPad Mini Retina (1st generation)
The iPhone 6s will definitely deliver better results. 


  While I cannot speak of the iPhone 5's audio performance, there has
  obviously been an improvement between the iPhone 4 to 6 with the
  ability to play 24-bit audio. The iPhone 6's DAC measures very well up
  to the maximum 48kHz samplerate.


In-depth review

To compare it against the iPad mini, just read some user complains about Audio Quality.

Though, the iPhone 6 didn't play High-res sounds. If this changed to the 6s, I cannot tell. This article from mashable suggests to use the external Lightning-to-USB adapter to plug in your own DAC to enhance the audio quality.

What's a fair point to make is, when you connect an external DAC to your iPhone 6s, you will have with no doubt a supreme audio experience. I don't know with which headphones you will plug in, but I am assuming the hardware wouldn't be a downer, more so the MP3 or audio file itself.