Best connection Mac Mini to Denafrips Pontus II

You’ve already got the Mac Mini, you should at least give it a try as a test. Mac Mini can sound pretty good in my experience! Especially the newer ones with the M series processors. 

I’m fairly sure you can’t connect HDMI in this case. Same physical connector but different format so it won’t work for music. I’d start with USB and spend some time listening. Use that as a baseline to grow from as you potentially upgrade some things. Maybe then try adding something like an iFi iPurifier3 which is an inline USB filter, I know people who use those with great results (and they are fairly cheap).

You could add a USB to HDMI converter like the Matrix, or one of the ones from Denafrips for a matching look. That may improve sound quality. Even so, I would spend time on regular USB first before adding an upgrade of that sort. That way you can better judge if it is helps or is worth the money.

One thing you could do would be to add a Denafrips Iris now to clean the signal from the Mini and run i2S into the Pontus, which also helps, and then add a better streamer later that you definitely wanna do.  Or you could get a better streamer now and add an Iris later for a nice performance bump down the road (I did this).  Option 1 costs less now if budget is an issue, but the bigger improvement will likely come from a better streamer.  Here are an Innuos Iris and Zen that if you can swing just get both now and be done with it — the performance improvement will be substantial.  Just one idea FWIW, and best of luck. 

https://www.usaudiomart.com/details/650268513-denafrips-iris-ddc/

https://www.usaudiomart.com/details/650246960-innuos-zen-mk3-4tb-storage/

What @soix said

The USB out from the Mac Mini will ultimately disappoint.  Seriously consider investing in an I2S renderer, like the Pi2AES Mercury.