While Río Lagartos [1] is somewhat downtrodden, San Felipe has well-maintained streets and sidewalks, brightly painted houses, and a clean, attractive waterfront promenade. The hotels and restaurants are nicer, and the atmosphere much more agreeable.
Hotel Posada La Hacienda (Calle 12 between Calles 15 and 17, tel. 986/862-2048, US$23 s/d with fan, US$28 s/d with a/c, US$32.50 t with fan, US$37 t with a/c) is a charming hotel just four blocks from the oceanfront. Rooms are nicely decorated in a Mexican style: adobe-colored tile floors, heavy wood furniture, and talavera sinks. They also are very clean. With cable TV, they are a steal in this part of the state.
Right on the waterfront, Hotel San Felipe (Calle 9 between Calles 14 and 16, tel. 986/862-2027, sanfelipehotel [at] hotmail [dot] com, US$34–43 s/d with fan, US$36–46 s/d with a/c) is a pleasant hotel with 18 rooms. Each room is slightly different, but all are clean and comfortable. Rooms with a view are especially nice, inside and out. If you fly fish and aren’t going to make it to Sian Ka’an or Xcalak, this hotel arranges recommended tours (US$250, 1–2 people, eight hours, including guide, lunch, and water).
The memorably named 
Restaurant El Popular Vaselina (The Popular Grease Restaurant, Calles 9 at Calle 12, tel. 986/862-2083, 11 a.m.–7 p.m. daily, US$4–10) serves excellent, super-fresh seafood in a big, airy dining area. Try the ceviche—usually an appetizer, the servings here are big enough to make a meal, and then some. Fronting San Felipe’s pleasant promenade, some of the tables have nice views and get a breeze off the water. Service is friendly and prompt.
The restaurant at Hotel San Felipe (Calle 9 between Calles 14 and 16, tel. 986/862-2027, 8 a.m.–9 p.m. daily, US$5–10) is another reliable choice, with longer hours.
San Felipe had no bank or ATM and no tourist office when we visited. A small clinic is on Calle 15 at Calle 10-A but was open 8 a.m.–1 p.m. and 5–8 p.m. Tuesday–Thursday only.
The Noreste bus terminal is on the main street entering town. It is closed when there is no bus leaving or arriving. Most buses departing Río Lagartos [1] stop here en route. There’s infrequent direct service to Cancún [2] and Mérida [3]; otherwise connect in Tizimín (US$2, one hour, seven departures daily).
If you’re driving, the cutoff to San Felipe is a few kilometers before entering Río Lagartos and well signed.
Links:
[1] http://www.moon.com/destinations/cancun-the-yucatan/the-state-yucatan/rio-lagartos-and-san-felipe/rio-lagartos
[2] http://www.moon.com/destinations/cancun-the-yucatan/cancun-cozumel-and-the-riviera-maya/cancun
[3] http://www.moon.com/destinations/cancun-the-yucatan/the-state-yucatan/merida