The potential for an island of stability is being seriously discussed. However, so far no such element has been found, which suggests they are not - or rarely - produced naturally.
What do you mean by unique molecules? How many different ways there are to arrange some or all of the atoms in the universe into a single molecule?
If you are looking for a purely mathematical answer of combinations it will involve huge factorials. It will also depend on how many ways you allow to arrange them. My basic statistic skills fail me here.
If you are looking for a realistic answer, there are two limits to the maximum size of any molecule: First, mass. If your molecule becomes too big, it will collapse into a sun, at which point I would no longer call it a molecule.
Second, abundance: Hydrogen and helium together are estimated (in Wikipedia) to account for 98% of all atoms. Hydrogen will often only bond to a single atom. So, no chains of hydrogen. Helium is even harder to get into any bond at all.
So, to get an estimate for the second case: Calculate how many DNA bases you can make from the atoms that are there. Then use the same kind of calculus as above for combining them. If your DNA string approaches the mass of, say, our sun, it’s probably no longer realistic.