I read somewhere about this kind of problem but I can't seem to find it now, so I'm going from memory.
Try placing the mic's close together at about a 90 degree angle from each other and at a 90 degree angle from the guitar. Then position yourself or the mics so they are about 2 - 3 feet away from the 12th fret.
microphone placement.JPG
The booming sound indicates that the mic(s) are getting sound straight from the soundhole, which is probably a bit to bassy for them to cope with, so experiment with aiming them more away from the soundhole towards the neck. This will reduce the bassy booming but might increase the sound of your fretting hand, and it might be hard to find the right compromise.
You could also try having the mics close to the ground and pointing upwards, or I have heard of people placing the mic(s) over their shoulder.
If you can manage to get a sound without too much booming you can always use EQ to reduce the bass whereas if you try to increase the treble it will just sound noisy.
If you would like you can always post me a recording and I will try to see what I can do with it, I've got plenty of spare time at the moment so it wouldn't be a problem.
In the meantime I'll see if I can find the original article for you. Good luck!