As the probability is the same in all cubes, we can calculate it in the cube $[-1,1]^3$.
We can limit ourselves to the sixth of the cube where $z$ is positive and has the greatest absolute value of the three coordinates. Then the radius of the sphere is $1-z$, and the centre of the cube is in the sphere if $x^2+y^2+z^2\le(1-z)^2$. Thus the admissible area of $(x,y)$ is the intersection of the square $[-z,z]^2$ with the circle $x^2+y^2=1-2z$. A corner of the square lies on the circle if $3z^2=(1-z)^2$, that is, $z=\frac{\sqrt3-1}2$, and a midpoint of the square lies on the circle if $2z^2=(1-z)^2$, that is, $z=\sqrt2-1$.
Thus, for $0\le z\le\frac{\sqrt3-1}2$, the entire square lies within the circle, so the area is $4z^2$.
For $\frac{\sqrt3-1}2\le z\le\sqrt2-1$ the circle and square intersect. The four segments of the circle that extend beyond the square each have area $(1-2z)\arccos\frac z{\sqrt{1-2z}}-z\sqrt{1-2z-z^2}$, so the area is $\pi(1-2z)-4\left((1-2z)\arccos\frac z{\sqrt{1-2z}}-z\sqrt{1-2z-z^2}\right)$.
For $\sqrt2-1\le z\le\frac12$ the entire circle lies within the square, so the area is $\pi(1-2z)$; and for $z\gt\frac12$ the area is $0$.
Thus the desired probability is
$$
\frac68\left(\int_0^\frac{\sqrt3-1}24z^2\mathrm dz+\int_\frac{\sqrt3-1}2^{\sqrt2-1}\left((1-2z)\left(\pi-4\arccos\frac z{\sqrt{1-2z}}\right)+4z\sqrt{1-2z-z^2}\right)\mathrm dz+\int_{\sqrt2-1}^\frac12\pi(1-2z)\mathrm dz\right)\;.
$$
The first and last integral evaluate to $\frac43\left(\frac{\sqrt3-1}2\right)^3=\sqrt3-\frac53$ and $\frac\pi4\left(1-2\left(\sqrt2-1\right)\right)^2=\pi\left(\frac{17}4-3\sqrt2\right)$, respectively. Wolfram|Alpha evaluates the indefinite form of the second integral to
$$
-\pi z^2+\pi z+4\sqrt{1-2z-z^2}\left(\frac{z^2}3+\frac z6-\frac56\right)+(6-z)\sqrt{1-2z-z^2}+\frac{15}2\arctan{\frac{1+z}{\sqrt{1-2z-z^2}}}+\frac12\arctan\frac{1-3z}{\sqrt{1-2z-z^2}}-4\arcsin\frac{1+z}{\sqrt2}+4(z-1)z\arccos\frac z{\sqrt{1-2z}}
$$
but refuses to evaluate it with limits. Substituting the limits by hand yields
$$
-\pi\left(3-2\sqrt2\right)+\pi\left(\sqrt2-1\right)+\frac{15}2\cdot\frac\pi2-\frac12\cdot\frac\pi2-4\cdot\frac\pi2=\left(3\sqrt2-\frac52\right)\pi
$$
at the upper limit and
$$
-\pi\left(1-\frac{\sqrt3}2\right)+\pi\cdot\frac{\sqrt3-1}2+\frac23-\sqrt3+\frac72\sqrt3-4+\frac{15}2\cdot\frac{5\pi}{12}+\frac12\left(-\frac\pi{12}\right)-4\cdot\frac{5\pi}{12}+4\cdot\frac{\sqrt3-3}2\cdot\frac{\sqrt3-1}2\cdot\frac\pi4=-\frac{10}3+\frac52\sqrt3+\frac{17}{12}\pi
$$
at the lower limit, so the second integral evaluates to
$$
\frac{10}3-\frac52\sqrt3+\left(3\sqrt2-\frac{47}{12}\right)\pi\;.
$$
Thus, the desired probability is
$$
\frac34\left(\sqrt3-\frac53+\frac{10}3-\frac52\sqrt3+\left(3\sqrt2-\frac{47}{12}\right)\pi+\pi\left(\frac{17}4-3\sqrt2\right)\right)\\=\boxed{\frac\pi4+\frac54-\frac98\sqrt3\approx0.086841}\;,
$$
in agreement with Aaron’s calculation and simulation.