Starting with the generating function:
$$\sum_{n=1}^\infty H_nx^n=-\frac{\ln(1-x)}{1-x}$$
replace $x$ with $-x$ then multiply both sides by $-\frac{\ln^3x}{6x}$ and integrate from $x=0$ to $1$ and use the fact that $-\frac16\int_0^1 x^{n-1}\ln^3xdx=\frac1{n^4}$ we get
$$\sum_{n=1}^\infty\frac{(-1)^nH_n}{n^4}=\frac16\int_0^1\frac{\ln^3x\ln(1+x)}{x(1+x)}dx=\frac16\mathcal{I}\tag1$$
$$\mathcal{I}=\int_0^1\frac{\ln^3x\ln(1+x)}{x(1+x)}dx=\int_0^\infty\frac{\ln^3x\ln(1+x)}{x(1+x)}dx-\underbrace{\int_1^\infty\frac{\ln^3x\ln(1+x)}{x(1+x)}dx}_{x\mapsto 1/x}$$
$$\mathcal{I}=\int_0^\infty\frac{\ln^3x\ln(1+x)}{x(1+x)}dx+\color{blue}{\int_0^1\frac{\ln^3x\ln(1+x)}{1+x}dx}-\int_0^1\frac{\ln^4x}{1+x}dx$$
By adding $\ \mathcal{I}=\int_0^1\frac{\ln^3x\ln(1+x)}{x(1+x)}dx=\int_0^1\frac{\ln^3x\ln(1+x)}{x}dx-\color{blue}{\int_0^1\frac{\ln^3x\ln(1+x)}{1+x}dx}\ $ to both sides, the blue integral nicely cancels out and we get
$$2\mathcal{I}=\int_0^\infty\frac{\ln^3x\ln(1+x)}{x(1+x)}dx-\int_0^1\frac{\ln^4x}{1+x}dx+\underbrace{\int_0^1\frac{\ln^3x\ln(1+x)}{x}dx}_{IBP}$$
$$2\mathcal{I}=\underbrace{\int_0^\infty\frac{\ln^3x\ln(1+x)}{x(1+x)}dx}_{\text{Beta function:}\ 6\zeta(2)\zeta(3)+6\zeta(5)}-\frac54\underbrace{\int_0^1\frac{\ln^4x}{1+x}dx}_{\frac{45}2\zeta(5)}$$
or
$$\mathcal{I}=3\zeta(2)\zeta(3)-\frac{177}{16}\zeta(5)\tag2$$
By plugging $(2)$ in $(1)$ we obtain that
$$\sum_{n=1}^\infty\frac{(-1)^nH_n}{n^4}=\frac12\zeta(2)\zeta(3)-\frac{59}{32}\zeta(5)$$
Bonus:
Following the same strategy, we can come up with two generalizations:
$$i)\int_0^1\frac{\ln^{2a-1}(x)\ln(1+x)}{x(1+x)}dx=\frac12\int_0^\infty\frac{\ln^{2a-1}(x)\ln(1+x)}{x(1+x)}dx+\frac{1+2a}2(2a-1)!\operatorname{Li}_{2a+1}(-1)$$
where the $\int_0^\infty$ integral can be done by beta function and $\operatorname{Li}_{a}(-1)=(2^{1-a}-1)\zeta(a)$.
Proof can be found here if needed.
$$ii)\int_0^\infty\frac{\ln^{2a}(x)\ln(1+x)}{x(1+x)}dx=(2a)!(2a+2)\left(1-2^{-2a-1}\right)\zeta(2a+2)$$
Its interesting to get the result of $ii$ without using beta function.
Edit
Details for evaluating $\displaystyle\int_0^\infty\frac{\ln^3x\ln(1+x)}{x(1+x)}\ dx$ using beta function can be found here. Another way is to start with subbing $\frac{1}{1+x}\mapsto x$
$$\int_0^\infty\frac{\ln^3x\ln(1+x)}{x(1+x)}\ dx=\int_0^1\frac{\ln^3\left(\frac{x}{1-x}\right)\ln x}{1-x}\ dx$$
$$=\int_0^1\frac{\ln^4x}{1-x}-3\int_0^1\frac{\ln^3x\ln(1-x)}{1-x}+3\underbrace{\int_0^1\frac{\ln^2x\ln^2(1-x)}{1-x}}_{IBP}-\underbrace{\int_0^1\frac{\ln x\ln^3(1-x)}{1-x}\ dx}_{IBP}$$
$$=\int_0^1\frac{\ln^4x}{1-x}-3\int_0^1\frac{\ln^3x\ln(1-x)}{1-x}+2\underbrace{\int_0^1\frac{\ln^3(1-x)\ln x}{x}}_{\large 1-x\to x}-\frac14\underbrace{\int_0^1\frac{\ln^4(1-x)}{x}\ dx}_{\large 1-x\to x}$$
$$=\frac34\int_0^1\frac{\ln^4x}{1-x}\ dx-\int_0^1\frac{\ln^3x\ln(1-x)}{1-x}\ dx$$
$$=\frac34(4!\zeta(5))+\sum_{n=1}^\infty H_n\int_0^1 x^n \ln^3x\ dx$$
$$=18\zeta(5)-6\sum_{n=1}^\infty\frac{H_n}{(n+1)^4}$$
$$=18\zeta(5)-6\sum_{n=1}^\infty\frac{H_n}{n^4}+6\zeta(5)$$
$$=18\zeta(5)-6[3\zeta(5)-\zeta(2)\zeta(3)]+6\zeta(5)$$
$$=6\zeta(2)\zeta(3)+6\zeta(5)$$