The best time to visit Merida is mid-September through mid-May, though there may still be a fair amount of rain in October and November. (It rains the most during the summer, but usually not often enough to spoil a vacation.) The Gulf of Mexico region is susceptible to hurricanes late July-early November.
Be prepared for higher humidity in Merida and at the inland archaeological sites in the Yucatan Peninsula. Summer temperatures there can hover around 100 F/38 C with near-100% humidity. The average coastal day temperatures year-round are in the 70s-80s F/23-32 C, with nights in the 60s-70s F/15-27 C. Take a sweater and umbrella, just in case.