We show by extensive numerical simulations and analytical variational calculations that elongated binary non-miscible Bose-Einstein condensates subject to periodic modulations of the radial confinement exhibit a Faraday instability similar to that seen in one-component condensates. Considering the hyperfine states of 87Rb condensates, we show that there are two experimentally relevant stationary state configurations: the one in which the components form a dark-bright symbiotic pair (the ground state of the system), and the one in which the components are segregated (first excited state). For each of these two configurations, we show numerically that far from resonances the Faraday waves excited in the two components are of similar periods, emerge simultaneously, and do not impact the dynamics of the bulk of the condensate. We derive analytically the period of the Faraday waves using a variational treatment of the coupled Gross-Pitaevskii equations combined with a Mathieu-type analysis for the selection mechanism of the excited waves. Finally, we show that for a modulation frequency close to twice that of the radial trapping, the emergent surface waves fade out in favor of a forceful collective mode that turns the two condensate components miscible.