My guess would be that the reproductive organs evolved as an internal offshoot to the digestive system. Originally fish would just need to squirt eggs and sperm out into the water, so it is more efficient and safer to just use the same hole (ie, the cloaca). The vast majority of animals still use a single entry for both reproductive and digestive functions. Even animals such as certain birds that have a pseudo-penis really just invert their cloaca and use the now external digestive tract to deliver sperm. It is only really the higher mammals that have split the reproductive entry from the digestive entry, so it is reasonable for the diverged organs to be anatomically located close by.
This question reminds me of a joke: Three engineers were discussing God in a pub. One said, God must be a mechanical engineer because the muscles and skeleton are such a finely tuned machine for movement. No said another, God must be an electrical engineer because the nervous system is an intricate circuit of electrical impulses. No said the civil engineer. God must be a civil engineer, who else would put a recreational zone next to a toxic waste dump?
It is hard to answer but I'd try...in tetrapods, notably newt (urodel) and mouse (mammal), primordial germ cells (PGC) originate from mesoderm by "epigenesis" (induction). The inducer is BMP signal. BMP signal is active in presumptive posterior part of the embryo, whereas presumptive anterior side of the embryo is protected by anti-BMP proteins (Noggin, Chordin, Cerberus). So, only the posterior part is "competent" to responde to BMP-inducing PGC. This may be also true for animals, like xenopus (anurs), where presumtive PGC originate in the posterior part of the embryo, in a "BMP active side". Notably, in xenopus, PGC arise by pre-formation mechanism (maternal determination) and transplantation of presumtive PGC in the anterior side of the embryo (where anti-BMPs proteins are active) abrogate PGC differentiation.
I'll not talk about PGC migration...
Generally, PGC originate in posterior part of the embryo and thus the reproductive system is located in the posterior part of the adult.
I advice you to read some paper of Surani MA (or let's download a review).
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