Pre-conquest America

Mayan

Me Oh Maya by Joe Scieszka 2003. (Time warp trio) . The three boys travel to Chichen Itza in 1000AD

Why there is no arguing in Heaven: a Mayan myth by Deborah Nourse Lattimore

Aztecs

Age of the Aztecs by Arantxa Barcenas (The Time Chronicles), 2014. Jurna and Austin find themselves in the last years of the Aztec empire on a search for an Aztec codex.
Aztec attack by Chris Blake, 2014 (Time Hunters series). An easy reader. Tom has to face the rain god Tlaloc and get back a missing treasure.The Flame of peace: a tale of the Aztecs by Deborah Nourse Lattimore
Aztec courage: a story about the Spanish conquest of Mexico by Al M Rocco, 2011. Told through the eyes of 14 year old Diego who sails with Cortez to Mexico.

The Comet of doom: a thrilling tale from the time of Moctezuma by Karen Wallace, 2009.  An easy reader set in the time just before the arrival of the Spanish.

The Sad Night: the story of an Aztec victory and a Spanish loss by Sally Schofer Matthews, 2001. Illustrated in the style of an Aztec codex, this tells the story of the Spanish conquest of Central America and one of the rare Aztec victories.

The time travelling cat and the Aztec sacrifice by Julia Jarman, Can Topher save Ka the cat from El Sol, rescue a girl from being sacrificed and escape from the floating city before it is destroyed.

Incas

Hualachi and the magic sandals by Juliet Heslewood, 1995. The story of the fastest runner of the Incas who lets his King down to perform an act of kindness.

Other locations

Lady of Palenque, flower of Bacal (Royal diaries) Mesoamerica 749

The Glass Knife by John Tully, 1974. Tio has been brought up to become the human sacrifice and what haens when he begins to susect the horrifying truth about the ceremony? Unspecified civilisation but possibly based on the Chimu.