The design of rare-earth-doped upconversion/downshifting nanoparticles (NPs) for theoretical use in nanomedicine has garnered considerable interest. Previous research has emphasized luminescent nanothermometry and photothermal therapy, while three-dimensional (3D) near-infrared (NIR) luminescent tracers have received less attention. Our study introduces Nd3+-, Yb3+-, and Ho3+-doped NaYF4 core-shell luminescent NPs as potential multiparametric nanothermometers and NIR imaging tracers. Nd3+ sensitizes at 804 nm, while Yb3+ bridges to activators Ho3+. We evaluated the photoluminescence properties of Nd3+-, Yb3+-, and Ho3+-doped core and core-shell NPs synthesized via polyol-mediated and thermal decomposition methods. The NaYF4:NdYbHo(7/15/3%)@NaYF4:Nd(15%) core-shell NPs demonstrate competitive nanothermometry capabilities. Specifically, the polyol-synthesized sample exhibits a sensitivity of 0.27% K-1 at 313 K (40 °C), whereas the thermally decomposed synthesized sample shows a significantly higher sensitivity of 0.55% K-1 at 313 K (40 °C) in the near-infrared range. Control samples indicate back energy transfer processes from both Yb and Ho to Nd, while Yb to Ho energy transfer enhances Ho3+-driven upconversion transitions in green and red wavelengths, suggesting promise for photodynamic therapy. Fluorescence molecular tomography confirms 3D NIR fluorescence nanoparticle localization in a biological media after injection, highlighting the potential of core-shell NPs as NIR luminescent tracers. The strategy's clinical impact lies in photothermal treatment planning, leveraging core-shell NPs for (pre)clinical applications, and enabling the easy addition of new functionalities through distinct ion doping.