Celestún Expeditions (in Mérida [1] 999/924-8283, celexp [at] sureste [dot] com) is operated by David Bacab, one of the region’s best-known bird-specialists and a longtime guide for the Celestún [2] area.
Besides the standard flamingo tour (using the official services, with Bacab as an additional guide) you can also take an early morning “bird walk”; a “butterfly walk” for those interested in the region’s numerous species of butterflies and moths; or a bike and kayak tour to the abandoned salt-producing village of Hacienda Real de Salinas and through the mangroves.
Also in Mérida, Ecoturismo Yucatán (Calle 3 between Calles 32-A and 34, Col. Pensiones, tel. 999/920-2772, www.ecoyuc.com.mx [3]) is one of several agencies that offer ecological tours to the area, especially for those interested in birding.
Links:
[1] http://www.moon.com/destinations/cancun-the-yucatan/the-state-yucatan/merida
[2] http://www.moon.com/destinations/cancun-the-yucatan/the-state-yucatan/celestun
[3] http://www.ecoyuc.com.mx