One of my greatest pleasures was the sailing of the river Santa María an Vaza Barras. Transportation from the small piers of Mosqueiro to Ilha de Goré and others are supported by powered canoes. You can rent it for a round trip to your destination for 30 reais or less (about 12 dollars) for two persons. Practical service with the invaluable bonus of the view and the pure air of the river.
To get one boat just bargain right on the piers of Mosqueiro.
The (right) choice of my company for my air transportation to Aracajú was Varig, almost the national airline of Brasil. From Buenos Aires to Río de Janeiro or Sao Paulo and later a transfer to Aracajú.
A long flight indeed (Brasil is really gigantic) but the services onboard were fine and the fleet is modern and safe.
Varig has flights to/from all America and Europe with connections to the rest of the world, so, take a look on their website and make your own arrangements for the pleasure of visiting this beautiful country.