The BEK family of flows have many important practical applications such as centrifugal pumps, steam turbines, turbo-machinery and rotor-stator devices. The Bödewadt, Ekman and von Kármán flows are particular cases within this family. The convective instability of the BEK family of rotating boundary-layer flows has been considered for generalised Newtonian fluids, power-law and Carreau fluids. A linear stability analysis is conducted using a Chebyshev collocation method in order to investigate the effect of shear-thinning and shear-thickening fluids for generalised Newtonian fluids on the convective Type I (inviscid crossflow) and Type II (viscous streamline curvature) modes of instability. The results reveal that shear-thinning power-law fluids have a universal stabilising effect across the entire BEK family of flows. However, the convective instability characteristics for the shear-thinning and shear-thickening Carreau fluids are affected by the value of the relaxation parameter k. The results reveal that Shear-thinning Carreau fluids have a small destabilising effect, while shear -thickening fluids have a slight stabilising effect on the Type I and Type II mode for the BEK family of flows when k =100. On the other hand, shear-thinning and shear-thickening Carreau fluids are found to have stabilising and destabilising effect, respectively for optimal relaxation value ko. The results are presented in terms of neutral curves and growth rates. Furthermore, an energy analysis is presented to gain insight into the underlying physical mechanisms behind the stabilising effects of generalized Newtonian fluids. In conclusion, the use of shear-thinning power-law and Carreau fluids with optimal value ko can be recommended to reduce skin-friction drag in enclosed rotor-stator devices for the entire BEK family of flows.