PHENIX has studied J / ψ production in s N N = 200 GeV collisions of p + p , d+Au, Au+Au and Cu+Cu collisions. This systematic study was designed to allow the extraction of hot nuclear matter effects on J / ψ production in heavy ion collisions after accounting for the baseline production cross section using p + p data, and for cold nuclear matter effects using d+Au data. Cold nuclear matter effects, for example gluon shadowing, are the effects associated with production of J / ψ from a nuclear target. The large yields obtained in the RHIC 2008 d+Au run provide, for the first time, an opportunity to characterize cold nuclear matter effects at RHIC, and try to isolate hot nuclear matter effects in Au+Au collisions. Low statistics preliminary measurements of excited charmonium yields and ϒ ( 1 S + 2 § + 3 S ) yields exist so far for p + p collisions, and there are preliminary results for ϒ production in d+Au collisions.