Using a simple quantum master equation approach, we calculate the Full Counting Statistics of a single electron transistor strongly coupled to vibrations. The Full Counting Statistics contains both the statistics of integrated particle and energy currents associated to the transferred electrons and phonons. A universal as well as an effective fluctuation theorem are derived for the general case where the various reservoir temperatures and chemical potentials are different. The first relates to the entropy production generated in the junction while the second reveals internal information of the system. The model recovers Franck-Condon blockade and potential applications to non-invasive molecular spectroscopy are discussed. ; Comment: extended discussion, to appear in NJP