Another apporach, using the binomial-theorem in a infinitely repeated application.
It has also the advantage, that it does not need the external knowledge of the value of $\zeta(-3)$ and also can be generalized to any positive power in the exponents of the series.
Consider a type of Vandermonde-vector $V(x)=[1,x,x^2,x^3] \quad $ . Then consider the upper triangular pascalmatrix of appropriate size
$$ P=\begin{bmatrix} 1&1&1&1\\ .&1&2&3 \\ .&.&1&3 \\ .&.&.&1 \end{bmatrix} $$
Then the matrixproduct holds $$V(x) \cdot P = V(x+1) $$
or, for example
$$\begin{matrix} & \cdot & \begin{bmatrix} 1&1&1&1\\ .&1&2&3 \\ .&.&1&3 \\ .&.&.&1 \end{bmatrix} \\ \begin{bmatrix}1 &3 &3^2&3^3 \end{bmatrix} &=&
\begin{bmatrix}1&4&4^2&4^3 \end{bmatrix} \end{matrix}$$
Because auf the properties of composition of linear operators we can write, for instance to sum four terms:
$$ V(x) \cdot (I - P + P^2 - P^3) = V(x) - V(x+1) + V(x+2)-V(x+3) $$
If it is now possible to express the infinite series of powers of P by the closed form for geometric series for matrices :
$$ I - P + P^2 - P^3 + ... - ... = (I + P)^{-1} = H $$
then we can make the ansatz and deduce formally:
$$ \begin{array} {rcl}
V(1) \cdot H &= &V(1) - V(2) + V(3) - ... + ... \\
& = & [1,1,1,1] - [1,2,4,8] + [1,3,9,27] - [1,4,16,64] +... - ... \\
& =& \begin{bmatrix}\eta(0), &\eta(-1), &\eta(-2), &\eta(-3) \end{bmatrix} \\
\end{array}$$
where $\eta(m)$ is the Dirichlet's eta-function.
The usability of the closed form for the geometric series also for the geometric matrix-series should be proven first - I do not attempt it here, but such proofs exist: you might follow for instance the chapter Neumann series in wikipedia, but there are a couple of other online resources too.
Here we simply use, that this ansatz works and we can now compute
H to dimension
4x4
$$ \small H= \begin{bmatrix} 2&1&1&1\\ .&2&2&3 \\ .&.&2&3 \\ .&.&.&2 \end{bmatrix} ^{-1} = \small \begin{bmatrix}
1/2 & -1/4 & 0 & 1/8 \\
. & 1/2 & -1/2 & 0 \\
. & . & 1/2 & -3/4 \\
. & . & . & 1/2
\end{bmatrix}$$
and then compute
$$ \small \begin{array}{} [1,1,1,1] \cdot H & =&\begin{bmatrix}1/2, & 1/4, & 0, & -1/8 \end{bmatrix} \end{array} $$
In the last column of the result-vector is the value $-\frac18 = \eta(-3)$ which you're asking for.
[update]: It might be interesting, that this scheme can even made be more convenient for the actual computation in that we do not need the explicite inverse
H.
First I show the - a bit lengthy- formal derivation and the simple computation scheme follows below.
Let's write $G=(I+P)$ because we do not need the inverse
H.
We can rearrange the matrix equation, writing
$$\small \begin{array}{rcl} Z&=&\begin{bmatrix}\eta(0), &\eta(-1), &\eta(-2), &\eta(-3) \end{bmatrix} \\ Z \cdot G& = &V(1) \\
Z \cdot (G - 2I)& =& V(1)-2Z \\
1 \cdot V(1) - Z \cdot (G - 2I)& =& 2Z \\
\text{ defining } \\
Z^*&=& \begin{bmatrix}1, \eta(0), &\eta(-1), &\eta(-2), &\eta(-3) \end{bmatrix} \\
G^*&=& \operatorname{concat}(V(1),-(G-2I)) \\
\text{ then it holds } \\
Z^* \cdot G^* &=& 2Z^*
\end{array}$$
But then $G^*$ is nilpotent, and powers of it degenerate to a form, where the first row remains nonzero only. If we choose a certain dimension
d for
G then on the lhs the entries in $Z^*$ become insignificant except the leading
1 and we can write:
$$ V(0) \cdot {G^*}^d = 2^d Z^* $$
That derivation shows, that we can use a repeated very simple doable matrix-multiplication to compute iteratively the sequence of $\eta(-k)$-values. We use the matrix
$$ \small G^* = \begin{bmatrix}
2 & 1 & 1 & 1 & 1 & 1 & 1 & \cdots \\
. & 0 & -1 & -1 & -1 & -1 & -1 & \cdots \\
. & . & 0 & -2 & -3 & -4 & -5& \cdots \\
. & . & . & 0 & -3 & -6 & -10 & \cdots \\
. & . & . & . & 0 & -4 & -10 & \cdots \\
. & . & . & . & . & 0 & - 5 & \cdots \\
. & . & . & . & . & . & 0 & \cdots \\
\vdots& \vdots& \vdots&\vdots&\vdots&\vdots&\vdots& \ddots\\
\end{bmatrix}$$
only to the required dimension(!) and compute iteratively (which can be done by paper&pen only) up to the d'th multiplication
$$ ([1,0,0,0...]\cdot G^*)\cdot G^* )\cdot \ldots )\cdot G^* = 2^d [1,\eta(0),\eta(-1),...,\eta(1-d), errors] $$
Since you mention, you'd like any input, you might also be interested in a more worked discussion of this here where I initially worked this out and extended the same principle also to non-alternating sums.