As is often the case, I must apologize for the length of the derivation below. In this case I needed to take great care that everything worked for complex parameters, which isn't my strong-suit.
The Laplace transform $\mathcal{L}$ of a function $f:\mathbb{R}_{>0}\rightarrow\mathbb{R}$ is given by the improper integral
$$\mathcal{L}_{t}{\left[f{\left(t\right)}\right]}{\left(s\right)}=\int_{0}^{\infty}\mathrm{d}t\,e^{-st}f{\left(t\right)},$$
for all $s\in\mathbb{C}$ such that the integral converges.
Our goal is to obtain as simple an expression as possible for the Laplace transform of $\operatorname{Ei}{\left(-y\right)}^{2}$, where the exponential integral $\operatorname{Ei}{\left(z\right)}$ is defined for complex argument by
$$\operatorname{Ei}{\left(z\right)}:=-\int_{-z}^{\infty}\mathrm{d}t\,\frac{e^{-t}}{t};~~~\small{z\in\mathbb{C}\setminus[0,\infty)}.$$
This will be accomplished in terms of polylogarithms.
Recall that for nonnegative order $n$, the polylogarithm of a complex argument may be defined iteratively by
$$\operatorname{Li}_{n+1}{\left(z\right)}:=\int_{0}^{z}\mathrm{d}t\,\frac{\operatorname{Li}_{n}{\left(t\right)}}{t};~~~\small{n\in\mathbb{Z}_{\ge0}\land z\in\mathbb{C}\setminus(1,\infty)\land\left(n\ge1\lor z\neq1\right)},$$
$$\operatorname{Li}_{0}{\left(z\right)}:=\frac{z}{1-z};~~~\small{z\in\mathbb{C}\land z\neq1}.$$
Integrating by parts $n$ times yields the following integral representation for the polylogarithm of positive order:
$$\operatorname{Li}_{n+1}{\left(z\right)}=\frac{(-1)^{n}}{n!}\int_{0}^{1}\mathrm{d}t\,\frac{z\ln^{n}{\left(t\right)}}{1-zt};~~~\small{n\in\mathbb{Z}_{\ge0}\land z\in\mathbb{C}\setminus(1,\infty)\land\left(n\ge1\lor z\neq1\right)}.$$
Also recall the dilogarithm obeys the following well-known functional relations:
$$\frac12\operatorname{Li}_{2}{\left(z^{2}\right)}=\operatorname{Li}_{2}{\left(z\right)}+\operatorname{Li}_{2}{\left(-z\right)};~~~\small{z\in\mathbb{C}\setminus(-\infty,-1)\cup(1,\infty)},$$
$$\operatorname{Li}_{2}{\left(z\right)}+\operatorname{Li}_{2}{\left(\frac{1}{z}\right)}+\frac12\ln^{2}{\left(-z\right)}=2\operatorname{Li}_{2}{\left(-1\right)}=-\operatorname{Li}_{2}{\left(1\right)};~~~\small{z\in\mathbb{C}\setminus[0,\infty)},$$
$$\operatorname{Li}_{2}{\left(z\right)}+\operatorname{Li}_{2}{\left(\frac{z}{z-1}\right)}+\frac12\ln^{2}{\left(1-z\right)}=0;~~~\small{z\in\mathbb{C}\setminus[1,\infty)}.$$
We will also make use of the following integration formula:
$$\int_{0}^{1}\mathrm{d}t\,\frac{b\ln{\left(1-at\right)}}{1-bt}=\operatorname{Li}_{2}{\left(a\right)}+\operatorname{Li}_{2}{\left(\frac{b}{b-1}\right)}-\operatorname{Li}_{2}{\left(\frac{a-b}{1-b}\right)};~~~\small{a\in\mathbb{C}\setminus(1,\infty)\land b\in\mathbb{C}\setminus[1,\infty)}.$$
Proof:
$$\begin{align}
\int_{0}^{1}\mathrm{d}t\,\frac{b\ln{\left(1-at\right)}}{1-bt}
&=-\int_{0}^{1}\mathrm{d}t\,\frac{b}{1-bt}\int_{0}^{1}\mathrm{d}x\,\frac{at}{1-axt}\\
&=-\int_{0}^{1}\mathrm{d}t\int_{0}^{1}\mathrm{d}x\,\frac{abt}{\left(1-axt\right)\left(1-bt\right)}\\
&=-\int_{0}^{1}\mathrm{d}x\int_{0}^{1}\mathrm{d}t\,\frac{abt}{\left(1-axt\right)\left(1-bt\right)}\\
&=-\int_{0}^{1}\mathrm{d}x\int_{0}^{1}\mathrm{d}t\,\frac{ab}{\left(ax-b\right)}\left[\frac{1}{1-axt}-\frac{1}{1-bt}\right]\\
&=-\int_{0}^{1}\mathrm{d}x\,\frac{1}{x\left(ax-b\right)}\left[b\int_{0}^{1}\mathrm{d}t\,\frac{ax}{1-axt}-ax\int_{0}^{1}\mathrm{d}t\,\frac{b}{1-bt}\right]\\
&=-\int_{0}^{1}\mathrm{d}x\,\frac{1}{x\left(ax-b\right)}\left[-b\ln{\left(1-ax\right)}+ax\ln{\left(1-b\right)}\right]\\
&=\int_{0}^{1}\mathrm{d}x\,\left[\frac{b\ln{\left(1-ax\right)}}{x\left(ax-b\right)}-\frac{a\ln{\left(1-b\right)}}{ax-b}\right]\\
&=\int_{0}^{1}\mathrm{d}x\,\left[-\frac{\ln{\left(1-ax\right)}}{x}+\frac{a\ln{\left(1-ax\right)}}{ax-b}-\frac{a\ln{\left(1-b\right)}}{ax-b}\right]\\
&=\int_{0}^{1}\mathrm{d}x\,\left[-\frac{\ln{\left(1-ax\right)}}{x}+\frac{a\ln{\left(\frac{1-ax}{1-b}\right)}}{ax-b}\right]\\
&=-\int_{0}^{1}\mathrm{d}x\,\frac{\ln{\left(1-ax\right)}}{x}+\int_{0}^{1}\mathrm{d}x\,\frac{a\ln{\left(\frac{1-ax}{1-b}\right)}}{ax-b}\\
&=\operatorname{Li}_{2}{\left(a\right)}+\int_{0}^{1}\mathrm{d}x\,\frac{a\ln{\left(\frac{1-ax}{1-b}\right)}}{ax-b}\\
&=\operatorname{Li}_{2}{\left(a\right)}+\int_{0}^{a}\mathrm{d}y\,\frac{\ln{\left(\frac{1-y}{1-b}\right)}}{y-b};~~~\small{\left[ax=y\right]}\\
&=\operatorname{Li}_{2}{\left(a\right)}+\int_{1-a}^{1}\mathrm{d}t\,\frac{\ln{\left(\frac{t}{1-b}\right)}}{1-t-b};~~~\small{\left[1-y=t\right]}\\
&=\operatorname{Li}_{2}{\left(a\right)}+\int_{\frac{1-a}{1-b}}^{\frac{1}{1-b}}\mathrm{d}u\,\frac{\ln{\left(u\right)}}{1-u};~~~\small{\left[\frac{t}{1-b}=u\right]}\\
&=\operatorname{Li}_{2}{\left(a\right)}+\int_{\frac{a-b}{1-b}}^{\frac{b}{b-1}}\mathrm{d}v\,\frac{(-1)\ln{\left(1-v\right)}}{v};~~~\small{\left[1-u=v\right]}\\
&=\operatorname{Li}_{2}{\left(a\right)}+\operatorname{Li}_{2}{\left(\frac{b}{b-1}\right)}-\operatorname{Li}_{2}{\left(\frac{a-b}{1-b}\right)}.\\
\end{align}$$
Suppose $s\in\mathbb{C}\land\Re{(s)}\ge-2$. We begin by using the integral representation of the exponential integral to rewrite the Laplace transform as a triple integral, and then change the order of integration:
$$\begin{align}
\mathcal{L}_{y}{\left[\operatorname{Ei}{\left(-y\right)}^{2}\right]}{\left(s\right)}
&=\int_{0}^{\infty}\mathrm{d}y\,e^{-sy}\operatorname{Ei}{\left(-y\right)}^{2}\\
&=\int_{0}^{\infty}\mathrm{d}y\,e^{-sy}\left[-\int_{y}^{\infty}\mathrm{d}x\,\frac{e^{-x}}{x}\right]^{2}\\
&=\int_{0}^{\infty}\mathrm{d}y\,e^{-sy}\left[\int_{1}^{\infty}\mathrm{d}t\,\frac{e^{-yt}}{t}\right]^{2};~~~\small{[x=yt]}\\
&=\int_{0}^{\infty}\mathrm{d}y\,e^{-sy}\int_{1}^{\infty}\mathrm{d}t\int_{1}^{\infty}\mathrm{d}u\,\frac{e^{-yt}}{t}\cdot\frac{e^{-yu}}{u}\\
&=\int_{0}^{\infty}\mathrm{d}y\int_{1}^{\infty}\mathrm{d}t\int_{1}^{\infty}\mathrm{d}u\,\frac{e^{-sy}e^{-yt}e^{-yu}}{tu}\\
&=\int_{0}^{\infty}\mathrm{d}y\int_{1}^{\infty}\mathrm{d}t\int_{1}^{\infty}\mathrm{d}u\,\frac{e^{-sy-yt-yu}}{tu}\\
&=\int_{0}^{\infty}\mathrm{d}y\int_{1}^{\infty}\mathrm{d}t\int_{1}^{\infty}\mathrm{d}u\,\frac{e^{-(s+t+u)y}}{tu}\\
&=\int_{1}^{\infty}\mathrm{d}t\int_{1}^{\infty}\mathrm{d}u\int_{0}^{\infty}\mathrm{d}y\,\frac{e^{-(s+t+u)y}}{tu}\\
&=\int_{1}^{\infty}\mathrm{d}t\int_{1}^{\infty}\mathrm{d}u\,\frac{1}{tu(s+t+u)}.\\
\end{align}$$
The inner integral in the double integral above is elementary, so we can reduce the Laplace transform to the following single-variable integral:
$$\begin{align}
\mathcal{L}_{y}{\left[\operatorname{Ei}{\left(-y\right)}^{2}\right]}{\left(s\right)}
&=\int_{1}^{\infty}\mathrm{d}t\int_{1}^{\infty}\mathrm{d}u\,\frac{1}{tu(s+t+u)}\\
&=\int_{1}^{\infty}\mathrm{d}t\int_{1}^{0}\mathrm{d}y\,\frac{(-1)}{y^{2}}\cdot\frac{1}{ty^{-1}(s+t+y^{-1})};~~~\small{\left[u=y^{-1}\right]}\\
&=\int_{1}^{\infty}\mathrm{d}t\int_{0}^{1}\mathrm{d}y\,\frac{1}{t\left[\left(s+t\right)y+1\right]}\\
&=\int_{1}^{\infty}\mathrm{d}t\,\frac{1}{t\left(s+t\right)}\int_{0}^{1}\mathrm{d}y\,\frac{\left(s+t\right)}{\left[1+\left(s+t\right)y\right]}\\
&=\int_{1}^{\infty}\mathrm{d}t\,\frac{1}{t\left(s+t\right)}\int_{0}^{1}\mathrm{d}y\,\frac{d}{dy}\ln{\left(1+(s+t)y\right)}\\
&=\int_{1}^{\infty}\mathrm{d}t\,\frac{\ln{\left(1+s+t\right)}}{t\left(s+t\right)}.\\
\end{align}$$
(Note: This is equivalent to the integral you found up to a single sign error out front.)
Then, assuming $\Re{(s)}>-1$, we have
$$\begin{align}
s\mathcal{L}_{y}{\left[\operatorname{Ei}{\left(-y\right)}^{2}\right]}{\left(s\right)}
&=s\int_{1}^{\infty}\mathrm{d}t\,\frac{\ln{\left(t+1+s\right)}}{t\left(t+s\right)}\\
&=s\int_{1}^{0}\mathrm{d}u\,\frac{(-1)u^{-2}\ln{\left(u^{-1}+1+s\right)}}{u^{-1}\left(u^{-1}+s\right)};~~~\small{\left[t=u^{-1}\right]}\\
&=\int_{0}^{1}\mathrm{d}u\,\frac{s\ln{\left(\frac{1+(1+s)u}{u}\right)}}{1+su}\\
&=\int_{0}^{1}\mathrm{d}u\,\frac{s\ln{\left(1+(1+s)u\right)}}{1+su}-\int_{0}^{1}\mathrm{d}u\,\frac{s\ln{\left(u\right)}}{1+su}\\
&=\operatorname{Li}_{2}{\left(-\frac{1}{1+s}\right)}-\operatorname{Li}_{2}{\left(-1-s\right)}-\operatorname{Li}_{2}{\left(\frac{s}{1+s}\right)}-\operatorname{Li}_{2}{\left(-s\right)}\\
&=\operatorname{Li}_{2}{\left(-\frac{1}{1+s}\right)}-\operatorname{Li}_{2}{\left(-1-s\right)}+\frac12\ln^{2}{\left(1+s\right)}\\
&=2\operatorname{Li}_{2}{\left(-1\right)}-2\operatorname{Li}_{2}{\left(-1-s\right)},\\
\end{align}$$
and thus,
$$\mathcal{L}_{y}{\left[\operatorname{Ei}{\left(-y\right)}^{2}\right]}{\left(s\right)}=\frac{2\operatorname{Li}_{2}{\left(-1\right)}-2\operatorname{Li}_{2}{\left(-1-s\right)}}{s};~~~\small{\Re{(s)}>-1}.\blacksquare$$
I'm quite confident you won't find a simpler expression than this. Cheers!