This article deals with intercropping of maize, squash and beans (the "Three Sisters") in Northeastern America rather than Mesoamerica but the principles should be similar.

The Three Sisters Mound System can also be seen as a complex knowledge system, which enabled Iroquoian farmers to develop an extensive, productive, and stable agricultural system. As an agronomist, I find that a careful analysis of the Thee Sisters reveals a crop and soil management system that is surprisingly sophisticated and rational. It provides for the essential elements of successful agricultural production in the northeast. The system enhances the soil physical and biochemical environment, minimizes soil erosion, improves soil tilth, manages plant population and spacing, provides for plant nutrients in appropriate quantities, and at the time needed, and controls weeds. In fact, the Three Sisters Mound System uses the same principles that agricultural scientists rely on today to develop recommendations for contemporary farmers. The practices are different, but the underlying principles that determine successful farming, in modern cropping systems and the Three Sisters are surprisingly similar. This chapter describes, from an agronomic perspective, the Three Sisters Mound System as it has been used in the Northeast (Figure 38-l). It begins by examining the mounds themselves and continues with the individual crops and their interactions to reveal the knowledge embodied in this indigenous agricultural system that explains its widespread use and productivity.

This source states that intercropping originated in Mesoamerica among the Maya but doesn't say exactly when.

So Mesoamerican agriculture did utilise intercropping, though whether the Olmec specifically did isn't stated.