Proof.
If we prove that any quasi-compact open of $X$ is affine, then $X$ is a separated scheme. Thus we may assume $X$ is quasi-compact and we aim to show that $X$ is affine. Cases (2) and (3) follow immediately from case (1) but we will give a separate proofs of (2) and (3) as these proofs use significantly less theory.
Proof of (3). Let $U$ be an affine scheme and let $U \to X$ be an étale morphism. Set $R = U \times _ X U$. The two projection morphisms $s, t : R \to U$ are étale morphisms of schemes. By Properties of Spaces, Definition 66.9.2 we see that $\dim (U) = 0$ and $\dim (R) = 0$. Since $R$ is a locally Noetherian scheme of dimension $0$, we see that $R$ is a disjoint union of spectra of Artinian local rings (Properties, Lemma 28.10.5). Since we assumed that $X$ is Noetherian (so quasi-separated) we conclude that $R$ is quasi-compact. Hence $R$ is an affine scheme (use Schemes, Lemma 26.6.8). The étale morphisms $s, t : R \to U$ induce finite residue field extensions. Hence $s$ and $t$ are finite by Algebra, Lemma 10.54.4 (small detail omitted). Thus Groupoids, Proposition 39.23.9 shows that $X = U/R$ is an affine scheme.
Proof of (2) – almost identical to the proof of (3). Let $U$ be an affine scheme and let $U \to X$ be a surjective étale morphism. Set $R = U \times _ X U$. The two projection morphisms $s, t : R \to U$ are étale morphisms of schemes. By Properties of Spaces, Definition 66.9.2 we see that $\dim (U) = 0$ and similarly $\dim (R) = 0$. On the other hand, the morphism $U \to \mathop{\mathrm{Spec}}(k)$ is locally of finite type as the composition of the étale morphism $U \to X$ and $X \to \mathop{\mathrm{Spec}}(k)$, see Morphisms of Spaces, Lemmas 67.23.2 and 67.39.9. Similarly, $R \to \mathop{\mathrm{Spec}}(k)$ is locally of finite type. Hence by Varieties, Lemma 33.20.2 we see that $U$ and $R$ are disjoint unions of spectra of local Artinian $k$-algebras finite over $k$. The same thing is therefore true of $U \times _{\mathop{\mathrm{Spec}}(k)} U$. As
\[ R = U \times _ X U \longrightarrow U \times _{\mathop{\mathrm{Spec}}(k)} U \]
is a monomorphism, we see that $R$ is a finite(!) union of spectra of finite $k$-algebras. It follows that $R$ is affine, see Schemes, Lemma 26.6.8. Applying Varieties, Lemma 33.20.2 once more we see that $R$ is finite over $k$. Hence $s, t$ are finite, see Morphisms, Lemma 29.44.14. Thus Groupoids, Proposition 39.23.9 shows that $X = U/R$ is an affine scheme.
Cohomological proof of (1). By Cohomology of Spaces, Lemma 69.10.1 we have vanishing of higher cohomology groups for all quasi-coherent sheaves $\mathcal{F}$ on $X$. Hence $X$ is affine (in particular a scheme) by Cohomology of Spaces, Proposition 69.16.7.
Geometric proof of (1). Choose a stratification
\[ \emptyset = U_{n + 1} \subset U_ n \subset U_{n - 1} \subset \ldots \subset U_1 = X \]
and étale morphisms $f_ p : V_ p \to U_ p$ as in Decent Spaces, Lemma 68.8.6 (we will use all their properties below). Then $\dim (V_ p) = 0$ by our definition of dimension of algebraic spaces. Thus Properties, Lemma 28.10.6 applies to each $V_ p$. Then $f_ p^{-1}(U_{p + 1}) \subset V_ p$ is quasi-compact open and hence is affine as well as closed. It follows that $|T_ p| \subset |U_ p|$ (see locus citatus) is open as well as closed. Hence $X$ is a disjoint union of open and closed subspaces whose reduced structures are schemes. It follows that $X$ is a scheme (Limits of Spaces, Lemma 70.15.3). Then the proof is finished by the case of schemes that we already referenced above.
$\square$
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