Here's an approach that uses Jordan canonical form. To begin, consider the case where $N \in M_n(\Bbb C)$ is a single Jordan block associated with $0$.
Denote $J_1 = J_1^{(n)} = \text{Id} + N$, which is the Jordan block of the same shape associated with $1$. Note that $J_1^r$ is similar to $J_1$. To see that this is the case, compute
$$
J_1^n = \pmatrix{1 & \binom{n}1 & \binom n2 & \cdots\\
0 & 1 & \binom n1 & \vdots\\
\vdots & \ddots & \ddots & \binom n1\\
0 & \cdots & 0 & 1 }
$$
where $\binom nk$ denotes a binomial coefficent. Note that $J_1^r$ has $1$ as its only eigenvalue and that the rank of $J_1^r - \text{Id}$ is equal to $n-1$. Conclude that the only possible Jordan form for $J_1^r$ is $J_1$.
Thus, there exists an invertible matrix $P$ such that $PJ_1^rP^{-1} = J_1$. However, this means that $(PJ_1P^{-1})^r = J_1$. Thus, the matrix $A_0^{(n)} := PJ_1P^{-1}$ satisfies $[A_0^{(n)}]^r = J_1^{(n)}$.
Now, consider an arbitrary nilpotent $N$. Note that $\text{Id} + N$ has 1 as its only eigenvalue, so its Jordan form can be written as
$$
Q^{-1}(\text{Id} + N)Q = \pmatrix{J_1^{(n_1)}\\ & \ddots\\ && J_1^{(n_k)}}
$$
for suitable $n_1,\dots,n_k$ with $n_1 + \cdots + n_k = n$. This Jordan-form matrix has an $r$-th root: denote
$$
\tilde A = \pmatrix{A_0^{(n_1)}\\ & \ddots \\ && A_0^{(n_k)}}.
$$
Verify that $\tilde A^r = Q^{-1}(\text{Id} + N)Q$. Thus, we have
$$
[Q \tilde A Q^{-1}]^r = \text{Id} + N.
$$
Thus, we have proved the desired result with $A = Q \tilde A Q^{-1}$.
An interesting alternative approach via the exponential map:
We can show that $\exp$ defines a bijection between the nilpotent and unipotent matrices. In particular, it suffices to consider the power series definitions of $\exp$ and $\ln$ in order to show that the functions $N \mapsto \exp(N) - I_n$ and $N \mapsto \ln(I_n + N)$ are inverse functions over the set of nilpotent matrices, noting that all power series over $N$ are finite by the nilpotency of $N$.
From there, we may find a nilpotent matrix $M$ such that $\exp(M) = \text{Id} + N$. The properties of the matrix expoenential ensure that $A = \exp(M/r)$ satisfies $A^r = \exp(M) = \text{Id} + N$, which is what we wanted.
A possible approach that avoids Jordan canonical form:
Outline: Suppose that $N^{k-1} \neq 0$ and $N^k = 0$. Take $A = \text{Id} + a_1 N + a_2 N^2 + \cdots + a_{k-1}N^{k-1}$. Expand $A^r$ and argue that there exist $a_1,\dots,a_{k-1} \in \Bbb C$ such that $A^r = \text{Id} + N$.
The argument for $r = 2$ would go along the lines of what I've laid out here.