Not everybody lives in the city, so not everybody can go to a city university. I'm sure if you applied to an accounting firm, especially on in the area where you are currently living, it wouldn't be an issue.
Generally, for firms hiring graduate accountants in cities like Sydney and Melbourne, the major factor is your ability to complete a CPA/CA once you start employment with them. JCU's Accounting degree does not allow for this. You can check on
http://www.charteredaccountants.com...Program/Entry-requirements/Accredited-courses to see what subjects are required. Now, their Master of Professional Accounting does allow for entry, but it may mean if you're living in Sydney/Melbourne once you graduate upper tier firms may be a bit more hesitant to hire you.
The reason JCU is much lower than top tiers like Melbourne and Sydney is because it's a regional university. This is the same for any regional university that isn't in a city. That doesn't mean their horrid, just demand is lower and access to facilities like you'd have in the city is reduced, thus they get lower rankings.
If it really makes a difference to you, then I would say move to Sydney. I guess it could prove your independence and responsibility and will allow for you to explore and grow. I'd suggest Brisbane, but sadly it appears all degrees from Queensland universities require a masters level before you can begin a CA
To do the JCU Masters is an extra 1.5 years full time. It's not a lot, but it is time that you won't be out working. I'd say, if you stay in Cairns, look around and see if you could get a traineeship or cadetship possibly. Work experience is something that will trump you over somebody that has no experience, even if they did go to a more "prestigious" university. You also learn so much more than you could at university, and I've found my working helps a lot. Even if you just do tax returns one or two days a week, it will look so much better for you than just attending a uni some people probably haven't heard of for 3 years.
If you do move to Sydney/Melb, these are also available more readily. You might find though that balancing work/life/study while in a brand new city with no close family and friends to fall back on is hard.
I hope that helps, and all the best deciding!