We report on synthesis and investigation of nanocrystalline cobalt-iron-pyrites with an emphasis on nanocrystal structure, morphology and magnetic behavior. The nanocrystals (NCs) were 5-25 nm in diameter as characterized using scanning electron microscopy (SEM) and transmission electron microscopy (TEM). With an increase in Fe fraction, X-ray diffraction and small-angle-X-ray scattering (SAXS) showed a systematic decrease in lattice constant, primary grain/NC size (15 to 7 nm), and nanoparticle (NP) size (70 to 20 nm), respectively. The temperature dependence of the DC magnetization and AC susceptibility versus frequency revealed a number of magnetic phases in Co x Fe1-x S2. Samples with x = 1 and x = 0.875-0.625 showed evidence of superspin glass (SSG) behavior with embedded ferromagnetic (FM) clusters of NPs. For x = 0.5, samples retained their mixed phases, but showed superparamagnetic (SPM) behavior with antiferromagnetic clusters suppressing magnetic dipolar interactions. Below x = 0.5, the pyrites show increasing paramagnetic character. We construct a phase diagram, which can be understood in terms of competition between the various dipolar, exchange, inter- and intracluster interactions. Our results suggest that NC size and shape can be tuned to engineer spin-polarized ferromagnetism of n-doped iron pyrite.