If you want something that won't pick at their gills I wouldn't recommend shrimp. I haven't tried regular ghost shrimp with them, but I know Amano shrimp will bother their gills.
If you want something that will be food later, I recommend zebra danios. They're cheap, active, and docile. Some smaller barbs or tetras (not tigers though) might work.
But if you want something more long term, we need to think about the size of an adult polypterus' mouth. Maybe something like tinfoil barbs or silver dollars. Other fish such as cichlids do well with adult polys, but those gills will be too tempting for them now.