To my knowledge, mushrooms were the primary shamanic element to their culture and was central to their religious beliefs. One thing I am not certain of, is whether the use of k'aizalah okox ("lost judgement mushroom") was restricted to a priestly class, or used throughout all levels of society. They also used the venom of Bufo alvarius, which was likely dried and then smoked.
So in modern terms 4-hydroxy-DMT, 4-phosphloroxy-DMT, 5-methoxy-DMT and Bufotenine would be the compounds the Mayans are believed to have used.
The area where the Mayans lived has one of the highest concentration of entheogenic plants known on the planet, so they could have used other substances as well, but most of the knowledge of Mayan culture has long since been destroyed.
One thing that I find interesting is that Terence McKenna and the Mayans both developed a seemingly similar concept of time and both Terence and the Mayans used psilocybe mushrooms extensively.
One example where you can see mushroom use in the historical record is the the Codex Vindobonesis. The Aztecs also used mushrooms ritualistically under the name Teonanacatl, ("Flesh of the Gods"), but thats fairly widely known in comparison to the use by the Mayan culture.