a couple of thoughts
how do each of the individual tracks sound? do they sound better solo'd than they do when all are playing? if so, you've prolly got a phase issue somewhere.
another thought (without knowing your space, where the amps are in relation to each other, etc) is that you've got some sort of comb filtering going on in the room between the two amps and the 3 mics. combined with phase issues (which could also happen depending where the mics and amps are placed in relation to each other--the NT1 5ft away capturing both amps concerns me--about both it and the relation of the two shures to each other), this could make ones tracks quite anemic. my guess is that you've got the two amps pretty much next to each other and you're playing though em both at the same time, eh?
if so, here's a thought--only play through one amp at a time, and if you have to have the sound of both amps, just record two tracks, one with each amp and pan em opposite each other. the combination of amps and the variations in each take should, generally speaking, give one a nice, fat sound. of course, 4-6 tracks of guitar (counting close and far mics on each amp) *should* be pretty damn fat.
it also could be an issue with your mic placement. how are you aiming the mics when they're against the amp grilles? are they pointed more towards the middle of the cone or the edge? how are they angled--pointing straight in or angled 45degrees? every minor change will affect your sound. experiment and find what works best. this WILL take some time. especially if you're working solo (engineering while playing).
it could be your room. what's it like and where do the amps sit in it? are some locations better than others? or you might have the wrong mics for the job. or the wrong guitar for the amp. or the wrong tone for the song (as aaron noted)....and remember, that a little distortion goes a LONG, LONG way when recording.....pile it on and you'll likely just get mud. you need a lot less than you need playing a gig.
it could also be something else in the guitar->amp signal chain. you told us about your recording gear (which should be plenty sufficient for getting a usable guitar sound), but what are you running in your guitar rig? if there's one thing that gives "proof in the pudding" about the true fidelities of ones guitar rig, it's sticking a mic in front of it.
hope this helps some and check back in.....
wade