Given the gear you listed, I'd guess you just need to get a grasp on gain staging. Somewhere in your signal chain, one gainstage is doing way too much work, and introducing noise in the process. None of your gear is too noisy to get a decent recording out of, but it's noisy enough to need to be setup properly to avoid too much noise.
The concept behind gain staging is that every part of the signal chain does it's share of the lifting, and no more. Any stage that works too hard will introduce noise and/or distortion. Any stage that does too little will make the following stage have too work too hard, introducing noise and/or distortion. Noise and distortion are passed on from whatever stage they start in, through the rest of the signal chain. So to troubleshoot the noise source, you start at the signal source (microphone in this case) and move through the preamp, any summing amps, out of the mixer and into the soundcard, through the soundcard software mixer, into the recording software, back out through the soundcard and through it's software mixer again, back into the Yamaha mixer and through whatever gain stages you're using there in monitoring, and finally through headphone amp or power amp. Work through that whole chain from the beginning, and figure out where in that process the noise is getting introduced.
Are you using insert outs from the channel pre on the MG?