We formulate a Chern-Simons composite fermion theory for Fractional Chern Insulators (FCIs), whereby bare fermions are mapped into composite fermions coupled to a lattice Chern-Simons gauge theory. We apply this construction to a Chern insulator model on the kagome lattice and identify a rich structure of gapped topological phases characterized by fractionalized excitations including states with unequal filling and Hall conductance. Gapped states with the same Hall conductance at different filling fractions are characterized as realizing distinct symmetry fractionalization classes.