Obviously, clean nails are better than dirty toilets and vice versa, therefore to remove doubt and clarify the context, I will present studies of how easy it is to keep each clean.
On the basis of the evidence presented above it is considered that toilet flushing is
sufficient to remove most of the microbial contamination from the toilet bowl, and the
surface of the bowl, provided that an adequate amount of water (minimum 15-17
litres of water) is used for flushing. Since toilet flushing does not achieve
decontamination under the flushing rim of the toilet, the toilet requires regular
application of a hygiene procedure which will maintain a low level of contamination in
the toilet bowl and under the flushing rim to prevent build up of biofilms or scale
which could harbour pathogens.
—source, page 55
The subungual region contains large numbers of bacteria which are largely inaccessible during hand hygiene practices and are therefore difficult to clean compared with the rest of the hands.
There are several reports linking fingernails with the transmission of nosocomial infection. One study linked an outbreak of postoperative Serratia marcescens infection with a nurse, suggesting that artificial fingernails may have facilitated the transfer of S. marcescens from home. In another study, an outbreak of Pseudomonas aeruginosa in a neonatal intensive care unit was associated with two nurses with long fingernails, one artificial and one natural.
It is therefore reasonable to conclude that nails are much more likely to contain pathogens than toilet seats, provided that a reasonable amount of cleaning is performed: hands are washed normally, toilets are flushed and hygenised as normal practice.