You are asking a seemingly simple question in a complex field.
yes, USB >> SPDIF (or its kissin' cousin, AES) - but only if its is implemented correctly. Or if the SPDIF is crummy (usually true) or....
So while i would begin with USB, you now need to make sure you have clean power, clean (isolated) ground and a DAC with a good clock since it is not the only thing with a meaningful impact on jitter. Most modern high end DAC do pay attention to both. How good they are of course varies.
If cables sounds different, there are serious problems. Some really are that bad, but its usually something else. Note that almost every "coax" SPDIF cable on the planet has an improper termination - RCA plug are almost never 75 ohm characteristic impedance.....and it just gets better :-)