You can compute these numbers for small $n$ and $r$ using Pólya's Enumeration Theorem (which is just a specific application of the orbit-stabiliser theorem).
A simple binary matroid of rank at most $r$ is simply a subset of the projective space $\mathrm{PG}(r-1,2)$ and isomorphism of binary matroids is precisely equivalence under the action of the group $G = \mathrm{PGL}(r,2)$.
Given the group you can calculate its cycle index polynomial which is a multivariate polynomial in variables $X_1$, $X_2$, $X_3$, $\ldots$
$$
Z(G;X_1, X_2, \ldots) := \frac{1}{|G|} \sum_{g \in G} \prod X_k^{n_k(g)}.
$$
where $n_k(g)$ is the number of cycles of length $k$ in the group element $g$.
Although this is defined as a sum over individual group elements, the expression is constant on conjugacy classes so all you need is something able to compute conjugacy classes.
Once you have this expression, you substitute $1+x^k$ for each variable $X_k$ and you end up with the generating function for the number of simple binary matroids of rank at most $r$.
If we do this for rank $r=4$ then we end up with
$$
x^{15}+x^{14}+x^{13}+2x^{12}+{\color{red}3x^{11}}+4x^{10}+5x^9 \\ +6
x^8+6x^7+5x^6+4x^5+3x^4+2x^3+x^2+x+1
$$
meaning that there are, for example, $3$ simple binary matroids of rank at most $4$ and size $11$.
How do you get the cycle index polynomial?
You can do it in GAP "by hand" using ConjugacyClasses
, but if you are fortunate enough to have a subscription to Magma, you can use the entirely undocumented function CycleIndexPolynomial
.
> g := PGammaL(4,2);
> cp := CycleIndexPolynomial(g);
> cp;
1/20160*x[1]^15 + 1/192*x[1]^7*x[2]^4 + 1/96*x[1]^3*x[2]^6 +
1/16*x[1]^3*x[2]^2*x[4]^2 + 1/18*x[1]^3*x[3]^4 +
1/6*x[1]*x[2]*x[3]^2*x[6] + 1/8*x[1]*x[2]*x[4]^3 +
2/7*x[1]*x[7]^2 + 1/180*x[3]^5 + 1/12*x[3]*x[6]^2 +
1/15*x[5]^3 + 2/15*x[15]
Here, Magma is using x[5]
for the variable $X_5$ and so on, and so you then have to substitute $1+x^5$ for $X_5$ and so on.
Here are the numbers of simple binary matroids of rank up to $6$ --- the size goes from 0 to 63 and it is reassuringly symmetric about the middle.
$$
\begin{array}{|rr|rr|rr|rr|}
0&1&16&29236&32&46875728&48&11780\\
1&1&17&70729&33&44065939&49&4708\\
2&1&18&164818&34&38939167&50&1907\\
3&2&19&366180&35&32339616&51&791\\
4&3&20&770299&36&25238329&52&340\\
5&5&21&1528238&37&18504126&53&155\\
6&10&22&2852575&38&12742321&54&72\\
7&19&23&5002828&39&8239590&55&35\\
8&35&24&8239590&40&5002828&56&19\\
9&72&25&12742321&41&2852575&57&10\\
10&155&26&18504126&42&1528238&58&5\\
11&340&27&25238329&43&770299&59&3\\
12&791&28&32339616&44&366180&60&2\\
13&1907&29&38939167&45&164818&61&1\\
14&4708&30&44065939&46&70729&62&1\\
15&11780&31&46875728&47&29236&63&1\\
\end{array}
$$