There are a few recent atomic partial charge schemes that are useful.
- You mentioned the electrostatic fitting schemes. These seek to best match the electrostatic potential of the molecule / system, but wouldn't be ideal for your situation. They have problems fitting charges on "buried atoms" such as the metal center of your complex, because they have little effect on the outer electrostatic potential (i.e. all your ligands surround the metal, so it's hard to separate the charge on the metal and the charges on the ligands).
- Atomic orbital partioning (e.g. Mulliken, NAO, etc.). These methods use atomic orbitals, but are often sensitive to basis set effects.
- Hirschfeld / Atoms in Molecules (AIM) analysis. These methods seek to partition the electron density to produce charges. Consequently, they'll have little problem with your metal complex. Several schemes exist depending on the program you use, but the open source Horton package can derive most by post-processing.
- A comment above suggests Thomas Manz's DDEC6 scheme. This has been fairly robust over the last few years although has fewer proponents than Hirshfeld / IBS approaches - possibly because Chargemol is currently the only program with an implementation.
Incidentally, there's an excellent review article "The Atomic Partial Charges Arboretum: Trying to See the Forest for the Trees" that may provide useful context.
In all, no single charge distribution tells the whole story, but a
trio of well‐defined ones – i.e., one representative each of the three
major classes of Corminboeuf and coworkers – should be able to cover
most aspects of it.
The three classes mentioned include electrostatic fitting, atomic orbital partitioning, and electron density partitioning.
For your purpose, I'd highly advocate some type of electron density partitioning - these methods are resistant to basis set effects and won't have issues with buried metal centers in your molecules.