To be isomorphic as finite dimensional vector spaces, you merely need to have the same dimension. A standard basis for $M_{m\times n}(k)$ should be clear, and has $mn$ elements. A standard basis for the other space consists of all maps $f_{ij}$, where $f_{ij}(\vec{e}_k)=\delta_{jk}\vec{e}_i$. So there is again a basis of $mn$ elements.
If $m=n$, then each vector space is actually an algebra, because you can `multiply' vectors together ang the result is a vector of the same type. With $n\times n$ matrices, the multiplication is matrix multiplication. With the linear functions space, composition is the multiplication. In this case the two algebras are indeed isomorphic, but a simple vector space isomorphism is not sufficient. It would need to be one such that $\phi(ab)=\phi(a)\phi(b)$. But the vector space isomorphism hinted at in the first paragraph (sending $f_{ij}$ to $1_{ij}$) will have this feature.