Is water a heterogeneous molecule?
I think you are confused. Heterogenous and homogeneous are words that are used to describe mixtures (of substances). In homogenous mixtures, the substances exist only in one phase, while heterogeneous mixtures the substances exist in two or more phases.

A molecule is homonuclear if it consists of atoms of a single chemical element ($\ce{O2}$). A molecule is heteronuclear if it is composed of more than one element ($\ce{H2O}$). Note that any pure molecule is considered a substance, and it is the combinations of these substances that form mixtures, either homogeneous, heterogeneous, or colloidal.