Polaritons enable subwavelength confinement and highly anisotropic flows of light over a wide spectral range, holding the promise for applications in modern nanophotonic and optoelectronic devices. However, to fully realize their practical application potential, facile methods enabling nanoscale active control of polaritons are needed. Here, we introduce a hybrid polaritonic-oxide heterostructure platform consisting of van der Waals crystals, such as hexagonal boron nitride (hBN) or alpha-phase molybdenum trioxide (α-MoO3), transferred on nanoscale oxygen vacancy patterns on the surface of prototypical correlated perovskite oxide SmNiO3 (SNO). Using a combination of scanning probe microscopy and infrared nanoimaging techniques, we demonstrate nanoscale real-time reconfigurability of complex hyperbolic phonon polaritons patterned at the nanoscale with unmatched resolution. Hydrogenation and temperature modulation allow spatially localized conductivity modulation of SNO nanoscale patterns, enabling robust real-time modulation and nanoscale reconfiguration of hyperbolic polaritons. Our work paves the way towards nanoscale programmable metasurface engineering as a new paradigm for reconfigurable nanophotonic applications facilitated by a hybrid material platform exploiting extreme light-matter interactions in polaritonic systems.