Coax or USB between transport and DAC?

I would use coax; USB connections appear to be more variable than coax.

If you're using USB, your source is a computer, and quality here depends in a big way on the USB implementation. Poor USB circuits at the DAC, when fed from a laptop, will get beaten by coax coming out of a decent CD transport. In my experience, most USB DACs under $1000 are limited to 16/48 over USB, and have poor implementation. To get really good sound, you need a decent USB/SPDIF converter, in most cases, unless you're spending over $1000 on the DAC. Suggestions on a DAC-only USB solution? Benchmark DAC-1 USB and Wyred for Sound DAC1 or 2 is where I would start.
I bought a PS Audio DLIII, and the laptop-DAC path via USB could not compete with my Denon changer as a transport. I bought a Vlink and the Jplay plug-in, now the sound is a little forward, but I have a wider soundstage, better depth, more detail. Planning on upgrading the converter.

I doubt your Pioneer transport can do USB? USB is only for computer sources and works very well or very poorly depending on the design of the DAC. Coax or toslink is what you'd be considering. Either can work very well.