Maranhão is far off the beaten track and very few birders visit the state. Coastal northern Maranhão is primarily waders and alike. The region around and just east of São Luis (and the Baía de São Marcos) is among the most important wintering sites in entire South America, but there are also a number of mangrove and/or coastal forest specialists such as Rufous Crab-Hawk, Scarlet Ibis, Golden-spangled Piculet and Plain-bellied Emerald. Other birding sites are primarily in the central, far south or west of the state (e.g. Kaempfer's Woodpecker has been seen near São Pedro da Água Branca). In the far west near the Rio Tocantins a wide range of river specialists can be seen, e.g. Glossy Antshrike, but little Amazonian forest remains there. Amazonian forests do remain elsewhere in the west (mainly in the Serra do Tiracambu area, where a wide range of Amazonian species such as the White-crested Guan and Pearly Parakeet still occur), but unfortunately deforestation has been pretty extreme in Maranhão (even by Amazonian standards). Drier Caatinga-like woodlands are scattered more or less throughout the state (e.g. near São João dos Patos), and species like Jandaya Parakeet, Hooded Gnateater (difficult without playback) and Ash-throated Casiornis are all fairly common. Sorry, little specific info, but years since I've been there last. If you go, best of luck as there's certainly plenty of possibilities, but finding specific up-to-date info will be very difficult.
I haven't spend any amount of time on "ordinary" boat tours on the Amazon, but in Brazil virtually all start from Manaus, which is pretty far from Maranhão. Nevertheless, some flights from countries further north are via Manaus, in which case you may be able to stop for a day or two. Loads of birding sites near Manaus.