Can't help with any location wise outside the Perth metro area, but FWIW, I would go all girls I think if I was sending my kids to boarding school. They go to a co-ed private school now, but if it was to be that extra step of boarding I would rather not have boys around. From what I understand through friends who have gone to all girls/all boys schools, they have a sister/brother school so there is still the opportunity for lots of social, sporting etc interaction with members of both sexes.

Not sure about the religious v. independent in terms of fees being higher for independent. Not sure you get any higher than (for girls) what they charge at Perth College, MLC or PLC and they're definitely religious based.