this series was evaluated by Cornel Valean here using series manipulation.
I took a different path as follows:
using the identity:$$\frac{\ln^2(1-x)}{1-x}=\sum_{n=1}^\infty x^n\left(H_n^2-H_n^{(2)}\right)$$ multiply both sides by $\ln^3x/x$ then integrate
$$-6\sum_{n=1}^\infty \frac{H_n^2-H_n^{(2)}}{n^4}=\int_0^1\frac{\ln^2(1-x)\ln^3x}{x(1-x)}\ dx$$ I was able here to find \begin{align} \sum_{k=1}^\infty\frac{H_k^{(2)}}{k^4}&=\frac43\zeta^2(3)-\frac23\sum_{k=1}^\infty\frac{H_k^{(3)}}{k^3}\\ &=\zeta^2(3)-\frac13\zeta(6) \end{align} as for the integral, it seems very tedious to calculate it using the derivative of beta function.
can we find it with or without using beta function?
This solution is by Cornel Valean.
Using the follwing identity: ( see Lemma $2(b)$ in this paper) $$\int_0^1x^{n-1}\ln^2(1-x)\ dx=\frac{H_n^2+H_n^{(2)}}{n}$$ and since $$\int_0^1x^{n-1}\ln^2(1-x)\ dx=2\sum_{k=1}^\infty\frac{H_{k-1}}{k}\int_0^1x^{n+k-1}\ dx=2\sum_{k=1}^\infty\frac{H_{k-1}}{k(n+k)}$$ Then $$\sum_{k=1}^\infty\frac{H_{k-1}}{k(n+k)}=\frac{H_n^2+H_n^{(2)}}{2n}\tag{1}$$ Divide both sides by $n^3$ then sum both sides from $n=1$ to $\infty$, we get \begin{align} S&=\color{blue}{\frac12\sum_{n=1}^\infty\frac{H_n^2}{n^4}+\frac12\sum_{n=1}^\infty\frac{H_n^{(2)}}{n^4}}=\sum_{k=1}^\infty\frac{H_{k-1}}{k}\left(\sum_{n=1}^\infty\frac{1}{n^3(n+k)}\right)\\ &=\sum_{k=1}^\infty\frac{H_{k-1}}{k}\left(\sum_{n=1}^\infty\left[\frac{1}{k^3}\left(\frac{1}{n}-\frac{1}{n+k}\right)-\frac1{n^2k^2}+\frac1{n^3k}\right]\right)\\ &=\sum_{k=1}^\infty\left(\frac{H_k}{k}-\frac{1}{k^2}\right)\left(\frac{H_k}{k^3}-\frac{\zeta(2)}{k^2}+\frac{\zeta(3)}{k}\right)\\ &=\sum_{k=1}^\infty\frac{H_k^2}{k^4}-\sum_{k=1}^\infty\frac{H_k}{k^5}-\zeta(2)\sum_{k=1}^\infty\left(\frac{H_k}{k^3}-\frac1{k^4}\right)+\zeta(3)\sum_{k=1}^\infty\left(\frac{H_k}{k^2}-\frac1{k^3}\right)\\ &=\sum_{k=1}^\infty\frac{H_k^2}{k^4}-\left(\frac74\zeta(6)-\frac12\zeta^2(3)\right)-\zeta(2)\left(\frac14\zeta(4)\right)+\zeta(3)\left(\zeta(3)\right)\\ &=\color{blue}{\sum_{k=1}^\infty\frac{H_k^2}{k^4}-\frac{35}{16}\zeta(6)+\frac32\zeta^2(3)} \end{align} Rearranging the blue sides, we get
where we used $\ \displaystyle\sum_{k=1}^\infty\frac{H_k^{(2)}}{k^4}=\zeta^2(3)-\frac13\zeta(6)\ $ (can be found in the same paper I linked or here)