Hi Mat,
There are a few options. You can modify the Basic Transport Package (.btn file), A15 Record to use a non-zero IFMTCN value to print concentrations to the standard output text file. See MT3DMS_manual.pdf, page 122 for these details.
Another method is to read the unformatted concentration (.ucn file) using a programming environment to process and/or output the array data into other custom formats. Flopy (a Python package) can read these:
from flopy.utils import UcnFile
ucn = UcnFile(r'C:\path\to\file.ucn')
concs = ucn.get_alldata()
concs[0].shape # (16L, 500L, 335L)
concs[0].max() # 0.013222964
...
There is plenty more that you can do with the NumPy arrays from here.
-Mike