The information you need can be found in On-Orbit Assembly, Modeling, and Mass Properties Data Book, Volume I & II, International Space Station Program, January 2008 (JSC 26557) (you need an updated version for more current data, here it's Revision AB).
First, the Space Station Analysis Coordinate System (SSACS) is defined as follows (see page 26):
The origin is located at the geometric center of the mid-ship
Integrated Truss Segment (ITS) S0. The longitudinal x-axis of multiple core modules, including the Zarya Functionalni Gruzvoi Blok (FGB) and Unity Node 1, is parallel with the analysis coordinate system axis XA, positive in the direction of the velocity vector. Positive YA axis runs parallel with the starboard truss from the center point at S0. Axis ZA completes the triad, pointing to the nadir.
The center of mass positions are then given in (see page 82)
Distance along X/Y/Z-axis from origin in SSACS
The largest part of this document is then devoted to giving you the information about the different configurations of the ISS. For example, for the configuration after the separation the shuttle during STS-132 (see page 542), you get:
Center of mass:
-4.37 m (-14.34 ft)
-.81 m (-2.66 ft)
3.43 m (11.25 ft)
Note that the document I linked above ends after STS-133 (early March 2011). That's after most of the assembly was finished, but about 8 t of equipment was since installed, most of it during STS-134, so you may have to look for a more current version of the document if you need high precision information on the current state of the station.