Problem is that spacecraft tend to be modular, like Apollo was, so it's hard to tell whether, for example, the Apollo Command and Service module combo was one spacecraft with disposeable parts, or two separate spacecraft.
You can make the case that the LM was the first true "spacecraft," but by the definition you've given, I think Mir probably qualifies best: AFAIK all manned spacecraft except Mir and the ISS have been launched in one piece on one launcher, meaning that they did operate in atmosphere at some point during their lives, whereas Mir and ISS were assembled in space, and Mir was the first of the two.
If you really want to be strict, I suppose the first spacecraft could be considered the first one for which no finished modules are launched from any gravitationally significant body, only building materials (nuts, bolts, sheet metal, electronics, etc.), and the whole thing is assembled in space.