What is an early reference for the fact that if a compact, connected $n$-manifold $M$ is covered by two open sets homeomorphic to $\mathbb{R}^n$ then $M$ is homeomorphic to $S^n$?
And is it true that if $M$ is a compact, connected $n$-manifold with boundary, and if $M$ is covered by two open sets homeomorphic to $\lbrace(x_1,\ldots,x_n) \in \mathbb{R}^n | x_n \ge 0\rbrace$, then $M$ is a closed ball?
I'll only discuss the first question (EDIT: Actually, I address the second question at the end). As Agol pointed out in the comments, for $n \geq 5$ this is an easy consequence of Newman's 1966 proof of the Poincare conjecture in the topological category.
I don't know if it was explicitly stated earlier than this. However, it can easily be derived from the main result of the paper
Brown, Morton, The monotone union of open (n)-cells is an open (n)-cell, Proc. Am. Math. Soc. 12, 812-814 (1961). ZBL0103.39305, MR0126835 (23 #A4129).
In fact, this works in all dimensions (including $3$ and $4$).
Brown's theorem is as follows. Assume that $M$ is a topological $n$-manifold and that for all compact $K \subset M$, there exists some open set $U \subset M$ with $K \subset U$ and $U \cong \mathbb{R}^n$. Then $M \cong \mathbb{R}^n$. Brown's proof is clever, but completely elementary.
To get the desired result from this, assume that $X = U_1 \cup U_2$ with $U_i \cong \mathbb{R}^n$ and that $X$ is compact. Let $\phi : \mathbb{R}^n \rightarrow U_1$ be a homeomorphism. It is enough to prove that $X \setminus \{\phi(0)\} \cong \mathbb{R}^n$. We will do this with Brown's theorem. Consider a compact set $K \subset X \setminus \{\phi(0)\}$. To verify Brown's criteria, it is enough to construct a homeomorphism $\psi : X \setminus \{\phi(0)\} \rightarrow X \setminus \{\phi(0)\}$ such that $\psi(K) \subset U_2$.
For $r>0$, let $B(r) \subset \mathbb{R}^n$ be the ball of radius $r$. The set $U_1 \setminus U_2$ is compact, so there exists some $R>0$ such that $U_1 \setminus \phi(B(R)) \subset U_2$. Also, there exists some $\epsilon > 0$ such that $K \cap \phi(B(\epsilon)) = \emptyset$. It is easy to construct a homeomorphism $f : \mathbb{R}^n \rightarrow \mathbb{R}^n$ such that $f(B(\epsilon)) = B(2R)$ and $f(0)=0$ and $f|_{\mathbb{R}^n \setminus B(3R)} = \text{id}$. We can therefore define a homeomorphism $\psi : X \setminus \{\phi(0)\} \rightarrow X \setminus \{\phi(0)\}$ by $\psi(p) = \phi \circ f \circ \phi^{-1}(p)$ for $p \in U_1 \setminus \{\phi(0)\}$ and $\psi(p) = p$ for $p \notin U_1$. Clearly $\psi(K) \subset U_2$.
EDIT: Lee suggested that this might be able to address his second question too. I thought a bit about it, and I believe that it can. The key is the following "relative" version of Brown's theorem, which can be proven exactly like Brown's theorem.
Theorem : Let $(M,N)$ be a pair consisting of a topological $n$-manifold $M$ and a closed submanifold $N \subset M$. Assume that for all compact $K \subset M$, there exists some open set $U \subset M$ such that $K \subset U$ and such that the pair $(U,U \cap N)$ is homeomorphic to the pair $(\mathbb{R}^n,\mathbb{R}^{n-1})$ (the second embedded in the standard way). Then $(M,N) \cong (\mathbb{R}^n,\mathbb{R}^{n-1})$.
To apply this, assume that $X$ is a compact manifold with boundary and that $X = U_1 \cup U_2$ with $(U_i,\partial U_i) \cong (\mathbb{R}^n_{\geq 0},\mathbb{R}^{n-1})$. Double $X$ to get a closed manifold $Y$, and let $Y' \subset Y$ be the image of the boundary of $X$. The open sets $U_i$ double to give an open cover $Y = V_1 \cup V_2$. Letting $V_i' = V_i \cap Y'$, we have $(V_i,V_i') \cong (\mathbb{R}^n,\mathbb{R}^{n-1})$. Let $(M,M')$ be the result of deleting the image of $0$ in $(V_1,V_1')$. It is enough to prove that $(M,M') \cong (\mathbb{R}^n,\mathbb{R}^{n-1})$, and this can be proven just like above.
Of course, Agol answered the second question first -- it follows from the topological Schonfleiss theorem applied to the double, which was proven by Brown in
Brown, Morton, A proof of the generalized Schoenflies theorem, Bull. Am. Math. Soc. 66, 74-76 (1960). ZBL0132.20002, MR0117695 (22 #8470b).
Mazur had earlier proven a weaker result. This requires the sphere to be bicollared, but this holds. Indeed, from the assumptions the sphere is locally bicollared, and Brown proved in
Brown, Morton, Locally flat imbeddings of topological manifolds, Ann. Math. (2) 75, 331-341 (1962). ZBL0201.56202, MR0133812 (24 #A3637).
that this implies that the sphere is bicollared. See
Connelly, R., A new proof of Brown’s collaring theorem, Proc. Am. Math. Soc. 27, 180-182 (1971). ZBL0208.50704, MR0267588 (42 #2490).
for a super-easy proof of Brown's collaring theorem.
