I'm not hearing any boomy 'noises' per se, but, yes, the recording itself is rather boomy at times and then seems to get tinny and then boomy again. Is the guitarist moving the guitar back and forth from the mikes? The boominess I'd think would be a result of the proximity effect and possibly of being too close to the 'sound hole' of the guitar. Basically, I think you're looking at a mike placement issue here. Out of curiosity, did you have the mikes directly connected to your computer (or sound card) or was there some type of intermediate interface like a mixing board?
Late reply here, but using some EQ might help. Try this.
Apply the Parametric Equalizer. Use these settings:
HP, 140Hz, 24dB/Oct
Band 1, 230Hz, -6dB, Q: 5.7
The HP filter attenuates the low frequency energy. A lot of the boominess is there, especially just above 100Hz and below. There are also some harmonics being generated, which are especially noticeable around 230Hz. It may be overkill to reduce that frequency for the entire track, but it helps a lot for the boomy areas - so I think it's worth cutting a bit there as well.
You may want to drop the high frequencies a bit around the 2-4khz region. They are especially noticeable with the above bass cuts.