If you're not restricting your search to software that is designed for geological applications only, you may find that the tools that are available in QGIS, R and ArcGIS might well provide what you need. As far as I'm aware, kriging was designed initially for the exact types of applications that you mention in your question, and the the implementations that are available in the software applications I mention above are designed to handle data from any generic xyz source, and for any spatial application, so I think these softwares might give you what you need.
If you're looking for freeware, then the Ordinary and Universal kriging tools that are provided in QGIS (download from qgis.org) may well give you what you need. The QGIS implementatinos are pretty basic in terms of parameterisation options, so R might well be preferable in this respect. I'm pretty sure that simple kriging and co-kriging are available in R also if required. If you have access to a licence for ArcGIS Geostatistical Analyst, this also provides a good range of options for parameterisation through a standard Arc type GUI interface.