The list of e.g. Entrez IDs, NCBI IDs, should be converted to UniProtKB or model organism database IDs, and those IDs used to search the GO database.
UniProt and PIR have similar ID mapping tools to help with the conversion:
GO annotations from QuickGO can be filtered for many parameters and provide mappings to several ID, e.g NCBI or Ensembl gene IDs: http://www.ebi.ac.uk/QuickGO/GAnnotation
The GO website has a list of taxa and authoritative database groups: http://www.geneontology.org/GO.annotation.species_db.shtml