All manifolds will be connected. Here is a quite large class of non-compact counter-examples that is hopefully intuitive: Let $M,N$ be two compact, oriented manifolds s.t. $H_1(M;\mathbb{Z})\neq0$ (in particular, $\pi_1(M)\neq1$), $\pi_1(N)\neq1$ and $n=\dim(M)+\dim(N)\ge3$. Let $X=M\times N-\{\ast\}$ be the non-compact $n$-manifold obtained by removing any point from $M\times N$. The S-vK theorem and $n\ge3$ implies that $\pi_1(X)=\pi_1(M\times N)=\pi_1(M)\times\pi_1(N)$ decomposes non-trivially. However, I claim that $X$ does not decompose non-trivially as a product of manifolds.
Proof Sketch: Assume $X=Y\times Z$ with $Y,Z$ of dimensions $0<r,s<n$ resp. That $X$ is non-compact implies that at least one of $Y$ and $Z$ is non-compact.
Assume $Y$ and $Z$ are both non-compact. There is a field $F$ s.t. $H_1(M;F)\neq0$, hence $H_{\dim(M)-1}(M;F)\neq0$ by Poincaré duality and the UCT. The Künneth theorem then implies that $H_{n-1}(M\times N;F)\neq0$ since it contains this group as a summand. However, orientability implies that $H_{n-1}(X;F)=H_{n-1}(M\times N;F)$. Now, applying the Künneth theorem to $X=Y\times Z$ yields that $H_{n-1}(X;F)=\bigoplus_{i+j=n-1}H_i(Y;F)\otimes_FH_j(Z;F)=0$. Indeed, $i+j=n-1$ implies $i\ge r$ or $j\ge s$ and this implies the vanishing of $H_i(Y;F)$ resp. $H_j(Z;F)$ by non-compactness. A contradiction.
Assume $Y$ is non-compact and $Z$ is compact. The $k$-th "homotopy group at infinity" $\pi_k^{\infty}(X)$ is, roughly speaking, the inverse limit of the homotopy groups $\pi_k(X\setminus K)$, where $K$ ranges over the compact subsets of $X$. The compact subsets $L\times Z$ with $L\subseteq Y$ compact are cofinal among these, so we obtain $\pi_k^{\infty}(X)=\pi_k^{\infty}(Y)\times\pi_k(Z)$. However, $X$ is locally Euclidean at infinity since $M\times N$ is a manifold, so $\pi_k^{\infty}(X)=\pi_k(S^{n-1})$. Together, it follows that $Z$ is $(n-2)$-connected, but $Z$ is a compact manifold of dimension $<n$, so it altogether has dimension $n-1$. Thus, $Y$ is a non-compact $1$-manifold, i.e. $Y=\mathbb{R}$, but $\mathbb{R}\times Z$ clearly has two ends whereas $X$ only has one. A contradiction.
(I would like to weaken the assumption $H_1(M;\mathbb{Z})\neq0$ to $\pi_1(M)\neq1$, but I have not been able to adapt the argument.)