Although this is a small city there are several options when thinking about staying overnight.
The Orizzonte Apart Hotel offers excellent accomodations with spectacular views of the Guanabara bay. This is a perfect option for someone looking for tranquiity and peaceful rest. You will need a car to move around since this hotel is located in the top of a hill standing by itself.
Solar do Amanhecer - Located in Charitas beach, this small and cozy hotel is nearby Sao Francisco beach with all the restaurants and shops that you might desire. It has ocean views and it is a walking distance of the new ferry boat station that connects Niteroi with Rio de Janeiro.
Tio Sam Hotel - This resort is situated in Camboinhas beach. It a new structure with comfortable rooms, swimming pools, gym, tennis courts... Steps to one of the most wonderful oceanic beaches of the city.