What is the best medical treatment for flat affect which may be due to depression and long standing schizophrenia.?

Individual treatment. You first deserve a good evaluation of your condition to be as sure as possible of diagnosis. If schizophrenia is the primary cause of the flat affect (which it can be), an important part of treatment will be antipsychotic medications. If you are more schizoaffective, then other medications might be needed in addition. Supportive therapy is helpful too. Your psychiatrist can suggest options.