More general terms:
* Substance: This is very broad but can encompass a molecule.
* Particle: This refers to any tiny bit of matter, including molecules.
* Chemical entity: This emphasizes the molecular composition.
More specific terms:
* Compound: If the molecule is made up of two or more different elements.
* Macromolecule: If the molecule is very large, such as a protein or DNA.
* Aggregate: If the molecule is part of a larger structure, like a cluster of molecules.
The best alternative will depend on the specific context of your writing.