USB vs. HDMI vs. Toslink

It depends on what you are using it with. Did you buy the Yggi or the Gungnir multibit? I think in audio only the optical is the lowest on the list. USB is what is normally used from a laptop. Depending on how high a sound quality you are shooting for a dedicated streamer will generally perform better than a laptop. 

While I plan on getting the Gungnir mb and Freya +, my current setup is laptop (jriver and HDtracks) > high quality hdmi > Yamaha tsr-7810 > Chord C line > Schiit Vidar > Speakers. The Yamaha doesn’t have any usb inputs sadly 

If you are using a laptop as a source, the best option you can probably do is to get a USB-to-S/PDIF re-clocker, such as the Wyred 4 Sound uLINK ($299). There are others, such as Singxer F1 ($200). Or go high end such as Audio-GD DI-20 ($550) or DI-20H ($1000). Or even Denafrips Gaia ($2300).

Then use a digital COAX cable to connect to your dac/receiver.  Or even BNC if you have the connections.

So while getting a converter is a good option for my current setup, when I get a new dac with a usb input, I would assume laptop > very nice usb > dac would be of better quality than laptop > very nice usb > converter > nice coax/bnc > dac?

Yes, a very high probability. Less is always more, and conversion is never a good thing.

It really depends on how good the USB receiver/clocker module is in your new "nice DAC".  If you get a DAC with a nice upgraded version of the Amanero USB module with good clocks and power supply, it could be better than a USB-to-SPDIF re-clocker. 

However, if you go with one of the high end models (Audio-GD or Denafrips Gaia), it is likely that these would be superior than what you find in a DAC. 

All DACs have to take the USB data packets, un-wrap the data and then clock the data at proper timing for the DAC (based on the sampling rate of your audio file - such as 44.1kHz, 48kHz, 96kHz, etc.).