A group (this includes the Doctor) of two, three or four is ideal IMO. Four and you sometimes have the issue of finding something for them all to do. Two and you sometimes have the issue of turning them into a double-act. I know Moffat said he always preferred the dynamic of a trio, but I couldn't find much evidence of that in his writing. Three would probably be my vote too though.
I'm not sure the wording of your options is very clear. "A duo" suggests the Doctor is one of them, which would be the same as your first option.