A good site for all of Brasil is
http://www.aluguetemporada.com.br/ if you don't mind navigating a site in Portuguese. It has an English link
http://www.homeaway.com/ but I haven't looked at that version so can't say if the content is exactly the same.
I've used the site 5 or 6 times for accommodation in Rio and once in Salvador.
My view is that for stays of less than 2 weeks for 1-2 people the hassle factor comes down on the side of staying in a hotel (although elite upgrades and Club access at the Sheraton and soon to be no longer Intecontinental Rio influence my judgement there)
For a stay of more than 2 weeks or if looking for more than one bedroom then flatstays really come into their own.