Certain sites (like Tulum and Chichén Itzá) are overrun with tourists from Cancún during the middle of the day (when their resort buses arrive). Try to see these sites in the morning or late afternoon. (Plus, it will be cooler then.) We found that it helped to get a hotel either at the site or just nearby. If we arrived at a site in the early evening we could check into our hotel, and show up at the ruins the first thing in the morning. We would then explore for a few hours, and when the heat and the tourists got too bad we would just go back to the hotel for a leisurely lunch. After lunch we would return to the site to complete our explorations at about the time when the tourist crowds were thinning out.
Insider tip: the pyramid of Kukulkan at Chichén Itzá (the big stepped pyramid seen in all the travel brochures) contains a smaller pyramid inside of it. There is an opening in the base of the outer pyramid that leads inside to a cramped humid stairway to a hidden chamber with some interesting statues. It is only open for an hour or so in the midday, and again in the late afternoon. Visit this passage in the later period, after the busloads of Cancún tourists have gone away.