Another museum about the first peoples of the area, in case you are not already satisfied with the Museu do Homen do Norte.
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Rio Negro Palace
Built by a German rich-man in the "golden age", the palace eventually became property of the government, which transformed it in a cultural center. Visits are free, being escorted by a staff-member is compulsory. Around the estate are manicured grounds and paths that culminate to the south at Parque Jefferson Peres, an impressive plaza of fountains, canals, and statuary close to the Rio Negro.
A church that is a special part of Manaus' heritage as it came about from a wife's vow in the late 19th century to have a chapel built in appreciation for the saint who supposedly interceded for her poor severely ill husband. The church is colloquially known as Capela de Pobra Diablo. Only open every June 13th.
Cultural space showing varying exhibits on Amazonian features (e.g. basket-weaving, botany, old Manaus tram car) as well as occasional performances.
Provincial Palace
This grand architectural specimen is also host to several museums, including the Museu de Arqueologia, the Pinacoteca do Estado (plastic arts center), Museu Tiradentes da Policia Militar (military police museum), Museu De Numismática Bernardo Ramos (numismatics), and an art museum. Get all your museum-viewing done in one shebang.
Heliodoro Balbi Square
Leafy plaza that is abutted by the Provincial Palace and Police Square.
Yet another Amazonia museum, this one in a colonial house, and curated by the public university. Nice baskets and masks and caiman skull collection.