To name a few, Dos Pilas, Mayapan, Xochicalco, Monte Alban, La Quemada, Becan, Cehache

I would check out the following publications for more information

1951 Mesoamerican Fortifications by Pedro Armillas. Antiquity (25):77-86

1973 Tepexi el Viejo: A Postclassic Fortified Site in the Mixteca-Puebla Region of Mexico by Shirley Gorenstein. Transactions of the American Philosophical Society New Series, Vol. 63, No. 1, pp. 1-75

When we are talking about Mesoamerican cities we are talking about more than 2000 years of history, so we should be careful not to generalize. Walls and fortifications did exist. In addition to the articles /u/Mictlantecuhtli provides, I've written previous comments about sieges during the Aztec era and the defenses of Tenochtitlan.

The Mayan city of Tulum had walls. According to the Canadian Museum of History city walls were rare for the Maya until late in their history.

Uxmal (Puuc region) and the impressive defensive works in the Petexbatun Region (Aguateca, Dos Pilas, Tamarindito). It is interesting how around 900AD, a lot of sites around Uxmal started building fortifications (Coba and smaller satellite sites).

I only know about Tenochtitlan, the capital of the Aztecs. The city was basically built in the middle of a chain of lakes, so the city was essentially protected by a "moat". The Aztecs built bridges to cross the water, so in the event of an invasion, all they needed to do was block the bridges to prevent an enemy from entering the city.

From Wikipedia:

It was connected to the mainland by causeways leading north, south, and west of the city. These causeways were interrupted by bridges that allowed canoes and other traffic to pass freely. The bridges could be pulled away, if necessary, to defend the city

Someone correct me if I'm wrong, but I believe the same logic was applied to Venice. Simply remove bridges that connect the city to the mainland and any invading army will be force to change their plan of attack.