We continue the investigation, started in [J. Stat. Phys. 166, 926-1015 (2017)], of a network of harmonic oscillators driven out of thermal equilibrium by heat reservoirs. We study the statistics of the fluctuations of the heat fluxes flowing between the network and the reservoirs in the nonequilibrium steady state and in the large time limit. We prove a large deviation principle for these fluctuations and derive the fluctuation relation satisfied by the associated rate function.