1

Paraty is very small so you can stay anywhere and still be within walking distance to all the attractions. I stayed at Backpacker's House by the bus station and that's a nice quiet hostel.

2

I second the recommendation for Backpacker's House. It's right next to the bus station, and the supermarket, and it's a short walk to the historic center/beach. The breakfast includes fresh fruit juices, a variety of fruits, coffee, bread, various spreads, and ham/cheese. The private double (R$50) faces onto the street and can be a bit noisy at night though, and the room/bathroom are a bit small.

Another nice place in Paraty is the Refron du Mar. It's located right on Praia do Pontal, which is one of the beaches in Paraty (about a 15 minute walk from the bus station). It's R$50 for a double; the room is spacious, and the ensuite bathroom is huge. My only complaint about the place was that the WiFi wasn't working very well.

In Rio, I stayed at the Che Lagarto Copacabana. The rooms/bathrooms were reasonably clean, although a bit cramped. It has a great location (3 blocks from the beach, 1 block from the metro), but it's definitely more of a party hostel, so I don't know if that's something you'd want