Depend what cancer stem cells you are looking for. For example, mammary CSC forms mammospheres when cultured in specific conditions, other CSC also form tumorspheres. Those spheres are considered to be form out of one CSC and by counting the number of spheres you can obtain the % CSC in your cells. In that way, you can study if the number of CSC is reduced o augmented after a certain treatment. You should check if your cells form these kind of spheres. Clonogenic assays can also give you a clue about changes in the proportion of CSC.
Many types of cancer stem cell - such as those from breast cancer - express high levels of Aldehyde dehydrogenase. These could be detected by Western blot, but the method of choice is an activity assay called the ALDEFLUOR kit, which is also evaluated by flow cytometry.