I am not sure what Schoen and Yau had in mind. Any open contractible $n$-manifold that is simply-connected at infinity is homeomorphic to $\mathbb R^n$. This is due to Stallings [1] if $n\ge 5$ and
to Guilbault [2] if $n=4$, while the case $n=3$ follows
from the result of Husch and Price [3] and the non-existence of fake $3$-cells
by Perelman's solution of the Poincaré conjecture.
[1] J.~Stallings, The piecewise-linear structure of Euclidean space, Proc. Cambridge Philos. Soc. 58 (1962), 481--488
[2] C.~R. Guilbault, An open collar theorem for $4$-manifolds, Trans. Amer. Math. Soc. 331 (1992), no.~1, 227--245.
[3] L.~S. Husch and T.~M. Price, Finding a boundary for a $3$-manifold, Ann. of Math. 91 (1970), 223--235.
Since the question is about dimension $3$ let me give more details. By Perelman there is no fake $3$-cells. Now Theorem 2 of [3] implies that any contractible $3$-manifold that is simply-connected at infinity is homeomorphic to the interior of a compact $3$-manifold $N$ (in fact the result in [3] gives a general criterion of when one can attach a boundary to a $3$-manifold). Now $N$ is a contractible $3$-manifold whose boundary is a $2$-sphere, and again invoking Perelman we conclude that $N$ is a $3$-disk, up to homeomorphism. Finally, by Moise homeomorphic $3$-manifolds are diffeomorphic.