Assuming you'll be ariving at the international airport (GRU), you'll either take a cab (get one from the booth, with the fixed rate - about R$ 75 - the airport is pretty far from the city so using the taximeter won't make a difference) or get one of airport buses. I'm not sure of the stops, though.
As for side trips, you can go to the beaches (Guarujá or Ubatuba), to the countryside or to the forest preserves (tropical forests on the hills - try Itatiai for some spectacular scenery). You really don't need a tour agency for that - just take a bus from the Tiete terminal and look for a pousada (simple hotel) when you get there.
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