In general, destinations south of Managua [1] are more developed for travelers, especially Granada [2] and San Juan del Sur [3], whose exploding number of colonial hotels, upscale surf camps, and convenient shuttle services have drastically altered the tourism landscape.
The rest of the country—north and east of Managua, and the Río San Juan [4] in the southeast—is a different story. In these places, with some basic Spanish, patience, and persistence, you can pueblo-hop on public buses till the Chontales cattle come home. Basic room and board are found in even small pueblos, as are community homestay and rural tourism programs.
Fancier hotels and restaurants are found in most department capitals, usually on or near the central plaza.
Most travelers begin in Granada and with good reason. It is smaller and more manageable than Managua and you can get a shuttle directly to Granada from the airport (under one hour). Granada is a beautiful, tranquil place to get acclimated to the heat and pace of things, and provides access to numerous day trips.
Links:
[1] http://www.moon.com/destinations/nicaragua/managua
[2] http://www.moon.com/destinations/nicaragua/granada
[3] http://www.moon.com/destinations/nicaragua/southwest-coast
[4] http://www.moon.com/destinations/nicaragua/rio-san-juan/down-the-rio-san-juan