Here are some examples, that should show you that there is a lot of countable toposes and lot of things in between finite sets and sets, too much to actually hope to list or classifies.
First as I said a lots of usual construction of Grothendieck toposes have a finistic version, which produces elementary toposes (in fact, bounded toposes over FinSet most of the time). For example given a finite category $C$ the category of finite presheaves on $C$ is a topos, in fact you can even take a topology and look at finite sheaves. You can have a look to chapter 5.2 in the third volume of Borceux's handbook of categorical algebra for some details on these.
If you have an inaccesible cardinal $\lambda$, then the category of sets of cardinality less than $\lambda$ is an essentially small elementary topos with a natural number objects.
As mentioned by Todd Trimble, elementary toposes are a bit weaker than ZF because they don't allow for unbounded replacement. concretely it means that you can construct essentially small full subcategory of the category of sets that are elementary topos without invoking an inaccessible cardinal. If you take any set $X$, the full subcategory of sets that appears as element of $\mathcal{P}^{n}(X)= \mathcal{P} (\mathcal{P}( \dots \mathcal{P}(X)) \dots )$ for some $n$ ($\mathcal{P}(X)$ being the set of subsets of $X$) is an elementary topos. If $X$ is finite, this is justs the category of finite sets, but if $X$ is infinite it will have a natural number object, but it will be uncountable. This produces a lot of concrete example of full subcategory of the category of sets that are small toposes.
Every time you have a model of ZF, its "category of sets" is a topos. Because of Löwenheim–Skolem there exists countable model of ZF, so this produces example of countable toposes admiting natural number objects.
There exists a "free topos" which admit a unique logical morphisms to any topos, and a "free topos with a natural number object" which admit a unique logical morphisms preserving the natural number object to any topos with a natural number object, see there as well as the reference given there for more details. It admit a syntactical description which shows that it is countable (informally: its objects can be describe as certain formula involving the operation that you have in a topos, like taking power objects and finite limits, and there is only a countable number of these, same for the maps).