A peaceful, lakeside community, San Miguelito has an interesting Casa de Cultura and access to the island of El Boquete. You can also venture up various rivers, into local wetlands, or over to Solentiname [1].
In town, stay at Hotel Cocibolca (tel. 505/2552-8803, $12), a tranquil hardwood building of 16 rooms, all with shared bath, and incredible sunset views of Ometepe [2]’s silhouette.
Just outside of town, the Finca el Cacao (tel. 505/8414-9927) offers a more bucolic stay, with cow-milking, crocodile-searching, monkey-watching, and similar, plus three meals a day for $35 per person.
One daily direct bus leaves Managua [3]’s Mayoreo at 7 a.m.; in San Carlos [4], ask at the bus station. You can also take the slow boat from Granada [5] and get off in San Miguelito before it reaches San Carlos.
Links:
[1] http://www.moon.com/destinations/nicaragua/rio-san-juan/the-solentiname-islands
[2] http://www.moon.com/destinations/nicaragua/ometepe-and-rivas/la-isla-de-ometepe
[3] http://www.moon.com/destinations/nicaragua/managua
[4] http://www.moon.com/destinations/nicaragua/rio-san-juan/san-carlos
[5] http://www.moon.com/destinations/nicaragua/granada