I know of the University of Pittsburgh where you can get a PhD in information science that focuses on Geoinformatics, which seems kind of cool.
I've been looking around but it seems that most PhD programs in Geography focus on either human or physical and don't really get into studying methods of GIS, which is what interests me.
I'm sure there are some that I'm missing though.
Beyond academia and some government positions, there is not a high demand for individuals who have their PhD in GIS. Many, but not all of the core fundamental principles of GIS are founded within human and physical geography (e.g. understanding the human/natural relationship, topography, scale, cartography, and statistics). I believe this question parallels the ongoing conversation/debate, is GIS a tool or a science? Here are some other universities offering a PhD in GIS.
It seems the UCL CENTRE FOR ADVANCED SPATIAL ANALYSIS (CASA) in London could fit your need.
And what about the Geographical Sciences and Urban Planning center of Arizona State University? is it to geographic for you ? I guess, looking for a PhD, you can discuss and keep some flexibility regarding the work you're doing.
By the way, the geomatic department of Laval University (Canada) could eventually interest you. I'm not sure they teach in english.
The University of Salzburg offers a "Doctoral College GIScience" and ten paid scholarships for predefined thesis topics, e.g. "Scalability and performance in near-real-time processing of geo-spatial data streams."
University of Maine has Spatial Information Science and Engineering which is pretty highly regarded in this field.
Some of the better "nuts and bolts" of GIS texts that I have read are authored by faculty there.
The University of Sherbrooke (Quebec) has a GIS PhD program. I'm told the classes are in French, but some students get by only speaking English.