(abridged) We present ALMA observations of hydrogen fluoride, HF J=1-0, H20 (220-211), and the 1.2 THz rest-frame continuum emission from the z=4.7 system BR1202-0725. BR1202-0725 is a galaxy group consisting of a QSO, a sub-millimeter galaxy (SMG), and two Ly-alpha emitters. We detected HF in emission in the QSO and possibly in absorption in the SMG, while water is detected in emission in both the QSO and SMG. The QSO is the most luminous HF emitter yet found and has the same ratio of HF emission line to infrared luminosity as a sample of local AGN and the Orion Bar. This consistency covers about 10 orders-of-magnitude in infrared luminosity, L_IR. Based on the conclusions of a study of HF emission in the Orion Bar and modeling, the HF emission in the QSO is either excited by collisions with electrons and H2 in molecular plasmas irradiated by the AGN and intense star formation or predominately by collisions with H2, with a modest contribution from electrons, in a relatively high temperature (~120 K), dense (~10^5 cm^-3) medium. Although HF should be an excellent tracer of molecular outflows, we do not find strong evidence for outflows in HF in either the QSO or the SMG. From a putative absorption feature in HF in the SMG, we estimate an upper limit on the outflow rate, dM/dt_outflow <~45 M_sun/yr. The ratio of the outflow rate to the star formation rate is <5% for the SMG. The broadness of the H2O line in the SMG, FWHM~1020 km/s, may suggest that either the gas on large scales (>4 kpc) is significantly more disturbed and turbulent due either to interactions and mass exchange with the other members of the group or to the dissipation of the energy of the intense star formation or both. The lack of significant molecular outflows in either source may imply that much of the energy from the intense star formation and AGN activity in this pair is being dissipated in their ISM.