I'm just about through Scooby-doo Mystery Inc, and they lean a bit on Mayan/Aztec storylines -- what a wonderfully evocative era that seems to have absolutely no hold on mainstream culture! Were there any Manga artists that glommed onto it? Western would be cool too, unless it's about gay Mayans (etc)
As a side-note, French comics (Bande dessinee) had a bunch of wonderful south american stuff, but the one torrent that collected thousands of them seems to be dead.
I know it's not a manga and not necessarily Mayan/Aztec related, but you might enjoy Inca and Inca II: Wiracocha, which are basically sci-fi Inca-based games.
Not going to bother trying to explain the complexity of them here, but I loved Inca II especially. It takes some serious twists and turns you just won't see coming and combines classic PC-style point-and-click puzzle solving with Tie Fighter/X-Wing style space combat. It's a visually crazy game and was just one of the many titles out back then that combined completely unique elements together into a very original story. Well worth checking out if you can stomach the old-school FMV sequences and visuals.