Substances - A Macroscopic Concept
It depends on the context

"Substance" is not a tightly defined term so the argument is largely linguistic not about chemistry. Unless, that is, you are talking about observable chemical properties and use the word. Then, the context of use matters and you might need to be careful in how the word is used.

With gases it doesn't much matter how much stuff you have as the individual molecules don't interact much. But for solids and liquids when you talk about "substance" the apparent chemical properties may depend on how many molecules or atoms you have. So you might need to be careful how many of the components are present. The reason why I say this is that some collections of small numbers of components have different properties to larger collections. 

Nanoparticles of gold, for example, have different properties to bulk metallic gold. Some show much stronger colours that metallic gold (eg small colloidal gold clusters are used to impart a red colour to some specialty glass products). So the small clusters have different properties to bulk gold and you don't see the bulk properties until the amount of gold is large enough.

So although the substance of both bulk gold and colloidal clusters of gold atoms might be said to be the same, it is probably better to be more specific and talk about colloidal clusters as being a different "substance" to bulk gold. But this isn't universally agreed as usage of substance is not precisely defined.

In short, if you are talking purely about what something is made from then the amount doesn't matter and you can say substance for any amount but if you are talkingg about the properties of the material it can be better to be specific as the properties do change with the amount of the components involved.