Near-field spectroscopy has been extensively applied recently to analyze collective optical properties of materials at the nanoscale. However, vibrations of small molecules were only recognizable in close proximity to a metallic resonator. We show that encapsulation in boron nitride nanotubes (BNNT) enhances the near-field vibrational spectra of C$_{60}$ fullerene, reaching a sensitivity limit of a few hundred molecules. Furthermore, products of chemical reactions inside the tubes can be identified, so long as their vibrational signatures lie in the polariton gap of the BNNT.