If you consider the number of papers published over the lifetime of IBM, and the fact that IBM Research does work in all levels of computing (materials science -> software), Microsoft's research output looks minuscule in comparison. But if you're considering only CS research, then you might be right.
On a similar note, Intel is another company that is very active in research and has published a significant amount of peer-reviewed publications. Samsung Research is yet another; they have an amazing presence at circuit design conferences, for instance.
Here is a nice snapshot of the major contributions that came out of IBM Research over the past 60 years: http://www.research.ibm.com/featured/history/. Edit: the invention of copper interconnects is enough for me to be frank (http://www-03.ibm.com/ibm/history/ibm100/us/en/icons/copperc...).
On a similar note, Intel is another company that is very active in research and has published a significant amount of peer-reviewed publications. Samsung Research is yet another; they have an amazing presence at circuit design conferences, for instance.