I have no idea at the moment where to find a reference for the specific result you seek. However, it can be deduced from the following facts:
Topological manifolds (paracompact and Hausdorff) are absolute neighbourhood retracts, and thus have the homotopy type of CW-complexes. This is briefly stated in corollary 1 of Milnor's article On spaces having the homotopy type of a CW-complex (published in Trans. Amer. Math. Soc. 90, 1959, pages 272-280). An extensive discussion of these matters is given in the thesis A topological manifold is homotopy equivalent to some CW-complex by Aasa Feragen.
The inclusion of the boundary of a manifold is a Hurewicz cofibration, as follows from the collaring theorem, proved by Morton Brown in Locally Flat Imbeddings of Topological Manifolds (published in the Annals of Mathematics, Second Series, Vol. 75, No. 2, 1962, pages 331-341). This result was later given a simpler proof by Robert Connelly in A new proof of Brown's collaring theorem, published in Proc. Amer. Math. Soc. 27, 1971, pages 180-182.
With these results at hand, we can now prove the result you state. Let $Y$ be a CW-complex admitting a homotopy equivalence $f : X \to \partial M$ to the topological manifold $\partial M$. Denote by $j : \partial M \to M$ the inclusion of the boundary of $M$, and factor the composition $$ X \overset{f}{\longrightarrow} \partial M \overset{j}{\longrightarrow} M $$ as the inclusion of a sub-CW-complex $i : Y \to X$ followed by a weak equivalence $h : X \to M$. The weak equivalence $h$ is a homotopy equivalence since both its domain and its target have the homotopy type of CW-complexes.
Finally, let me briefly justify why we can take $i : Y \to X$ above to be the inclusion of a subcomplex of a CW-complex. The usual construction produces $(X,Y)$ as a relative CW-complex, i.e. $X$ is obtained from $Y$ by adding cells in increasing order of their dimension. Now observe that this construction can be modified to produce $X$ as a CW-complex itself: at each stage of the construction of $X$, we can replace the attaching maps of the cells with cellular maps via the cellular approximation theorem.