Is there any established genealogy of the deities of these two civilizations? Are the origins of at least some of the deities explained anywhere, perhaps in a creation myth at least, even if no detailed ancestry is available? It appears that much of this information has been lost or is only available in a few contradictory fragments. Maybe a specialist on these cultures can shed abit more light.
For the Aztecs I recommend looking at two books from La Historia Universal de las Cosas de Nueva España (in English: the Universal History of the Things of New Spain AKA the Florentine Codex) by Franciscan friar Bernardino de Sahagún. The Codex was compiled and written beginning in the mid 16th century a few decades after the conquest of Tenochtitlan. Book 1 is titled The Gods and goes into details the various gods worshipped by the Aztec. Book 3 covers the Origin of the Gods and their various myths. English translations of the Codex were made by Charles Dibble and Arthur Anderson.
For the Maya I would recommend starting with Maya Cosmos Three Thousand Years on the Shaman's Path (1993) by David Freidel, Linda Schele, and Joy Parker. It is an older text that was written shortly after Maya researchers were able to translate Maya hieroglyphs, but it provides a good base to work from as you read newer literature that incorporates more research and information. After that text you may want to read Recovering the past: Classic Maya language and Classic Maya gods (1999) by David Stuart, Stephen Houston, and John Robertson and maybe An illustrated dictionary of the gods and symbols of ancient Mexico and the Maya (1997) by Karl Taube. Unfortunately for Maya researchers there is no one pre-Columbian or post-conquest piece of literature to draw from. Instead they must rely on brief texts carved into stone or painted on ceramics coupled with art imagery to get an idea of who the Maya worshipped.