The first sum $S_1$:
From this solution we have
$$I=\int_0^1\frac{\operatorname{Li}_3(x)}{1+x^2}\ dx=\frac1{384}\left(\psi^{(3)}\left(\frac14\right)-8\pi^4-9\pi\zeta(3)-64\pi^2G\right)\tag{1}$$
But
\begin{align}
I&=\sum_{n=0}^\infty(-1)^{n}\int_0^1 x^{2n}\operatorname{Li}_3(x)\ dx, \quad \text{apply integration by parts}\\
&=\sum_{n=0}^\infty(-1)^{n}\left(\frac{\zeta(3)}{2n+1}-\frac{\zeta(2)}{(2n+1)^2}+\frac{H_{2n+1}}{(2n+1)^3}\right)\\
&=\frac{\pi}4\zeta(3)-G\zeta(2)+\sum_{n=0}^\infty(-1)^n\frac{H_{2n+1}}{(2n+1)^3}\tag{2}
\end{align}
From (1) and (2) we get
$$\sum_{n=0}^\infty(-1)^n\frac{H_{2n+1}}{(2n+1)^3}=\frac1{384}\psi^{(3)}\left(\frac14\right)-\frac{1}{48}\pi^4-\frac{35}{128}\pi\zeta(3)$$
Or
$$S_1=\sum_{n=1}^\infty (-1)^{n-1}\frac{H_{2n+1}}{(2n+1)^3}=1+\frac{35}{128}\pi\zeta(3)+\frac{1}{48}\zeta(4)-\frac1{384}\psi^{(3)}\left(\frac14\right)$$
The solution for the second sum $S_2$ is by Cornel Valean and as follows:
By Cauchy product we have
$$\operatorname{Li}^2_2(x)=\sum_{n=1}^\infty x^n\left(\frac{4H_n}{n^3}+\frac{2H_n^{(2)}}{n^2}\right)-6\operatorname{Li}_4(x)$$
set $x=i$ and take the imaginary parts of both sides we have
$$\Im\sum_{n=1}^\infty(i)^n\frac{H_n^{(2)}}{n^2}=\frac12\Im\operatorname{Li}^2_2(i)+3\Im\operatorname{Li}_4(i)-2\Im\sum_{n=1}^\infty(i)^n\frac{H_n}{n^3}$$
Using the fact that
$$\Im\sum_{n=1}^\infty (i)^n a_n=\sum_{n=0}^\infty (-1)^n a_{2n+1}$$
we have
$$\sum_{n=0}^\infty(-1)^n\frac{H_{2n+1}^{(2)}}{(2n+1)^2}=\frac12\Im\operatorname{Li}^2_2(i)+3\Im\operatorname{Li}_4(i)-2\sum_{n=0}^\infty(-1)^n\frac{H_{2n+1}}{(2n+1)^3}$$
substitute $\sum_{n=0}^\infty(-1)^n\frac{H_{2n+1}}{(2n+1)^3}=\frac1{384}\psi^{(3)}\left(\frac14\right)-\frac{1}{48}\pi^4-\frac{35}{128}\pi\zeta(3)$ along with $\Im\operatorname{Li}^2_2(i)=-\frac{\pi^2}{24}G$ and $\Im\operatorname{Li}_4(i)=\frac1{768}\psi^{(3)}\left(\frac14\right)-\frac{\pi^4}{96}$ we get
$$\sum_{n=0}^\infty (-1)^{n}\frac{H_{2n+1}^{(2)}}{(2n+1)^2}=-\frac18G\zeta(2)+\frac{35}{64}\pi\zeta(3)+\frac{15}{16}\zeta(4)-\frac1{768}\psi^{(3)}\left(\frac14\right)$$
Or
$$S_2=\sum_{n=1}^\infty (-1)^{n-1}\frac{H_{2n+1}^{(2)}}{(2n+1)^2}=1+\frac18G\zeta(2)-\frac{35}{64}\pi\zeta(3)-\frac{15}{16}\zeta(4)+\frac1{768}\psi^{(3)}\left(\frac14\right)$$