With a large raised patio overlooking the lagoon [1], La Pirámide (Calle Principal at Laguna Cobá, no phone, 7:30 a.m.–9 p.m. daily, US$5–14) is a nice place for lunch après-ruins or beer and snacks in the evening. The restaurant receives a number of tour groups, and it often has a buffet set up (US$11); otherwise, the menu has grilled fish, chicken, and meat dishes as well as typical Mexican fare.
A few doors down and just before the entrance to Villas Arqueológicas, Nicte Ha (facing Laguna Cobá, tel. 984/206-7025, 8 a.m.–7 p.m. daily, US$3–8) is a small place serving tacos, enchiladas, and various pork dishes. The name Nicte Ha (Flower of the Water) may refer to the eyes of hungry crocodiles in the lagoon; tour group leaders often try to wow their charges by luring the crocs to shore—raw chicken is a favorite, apparently.
The restaurant at Villas Arqueológicas Cobá (tel. 984/206-7000, 7:30 a.m.–10 p.m. daily, US$6–16) is comfortable and quiet, and has the best selection in town, including pasta, seafood, and Yucatecan dishes.
Across the street from a peach-colored church, Abarrotes Neftali (Calle Principal s/n, 7 a.m.–11 p.m. daily) is a minimart that sells canned goods, bread, and some fresh produce.
Links:
[1] http://www.moon.com/destinations/cancun-the-yucatan/cancun-cozumel-and-the-riviera-maya/tulum-and-southern-quintana-roo/coba/other-sights