According to the IUPAC Gold Book a molecular entity is "any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity".
Molecular entity is used as a general term for any singular entity, irrespective of its nature, in order to concisely express any type of chemical particle that can exemplify some process: for example, atoms, molecules, ions, etc. can all undergo a chemical reaction.
Chemical species is the macroscopic equivalent of molecular entity and refers to sets or ensembles of molecular entities.
Again from IUPAC: "The degree of precision necessary to describe a molecular entity depends on the context. For example 'hydrogen molecule' is an adequate definition of a certain molecular entity for some purposes, whereas for others it is necessary to distinguish the electronic state and/or vibrational state and/or nuclear spin, etc. of the hydrogen molecule."