To search the GO database, a list of Entrez IDs, NCBI IDs, etc. needs to be converted to UniProtKB or model organism database IDs. If you’ve found yourself with a set of genes/gene products but you need to convert the identifiers, you can try the tools from UniProt or the Protein Information Resource (PIR):
GO annotations from QuickGO can be filtered for many parameters and provide mappings to several IDs, e.g NCBI or Ensembl gene IDs: QuickGO