At the international airport there are two offices right to the right of the main terminal, these offices house the domestic airlines. These are great if you want to get to the Atlantic Coast. Prices change but it takes 1.5 hours to get to the Corn Islands as opposed to a full day overland. If you are trying to save time, then this is the best way to get to the Corn Islands or anywhere on the Atlantic Coast.
Boat is the only way to get to the Isla de Ometepe or to the Solentinames. Be aware that high winds and bad weather can cancel ferry trips. That might not be such a bad thing, though, since windy/bad weather can make the Ferry trip unpleasant for those prone to seasickness, and many of the boats used to access Ometepe are old, smaller ferries and launches. The fastest route to Ometepe leaves from San Jorge 10 minutes from Rivas and often connecting on the same Managua-Rivas bus and goes to Moyogalpa. A much longer trip can be taken and with only a couple of trips weekly from Granada to Altagracia. There is a large modern ferry from San Jorge that makes daily trips to the new port of San Jose del Sur close to Moyogalpa.
Boat is also a cool way to get to the Corn Islands. Take a bus to Rama, which is the end of the road. This road used to be rough and hard, but it has now been newly paved and makes the trip easier 2006. There is a weekly ship with bunk beds to the Corn Islands, and small launches to Bluefields and El Bluff multiple times a day. Or you can get on a speedboat to Bluefields or El Bluff. Catch the boat to the Corn Islands from there, or take a flight out of Bluefields. Also, a large cargo boat takes two days returning from the Corn Islands to Rama with an overnight in El Bluff to take on cargo. There is now also a road from Rama to Pearl Lagoon, which can also be reached in a launch from Bluefields.
The taxi drivers in Managua can be aggressive and there are loads so it is easy to find a fare that suits you. Taxis will take multiple fares if they are heading roughly in the same direction. Taxi drivers in all the cities are generally fair and well mannered and a nice way to see local scenery. For fares within smaller cities there is a set fare per person, so no negotiating is needed. In Managua the fare should be negotiated before getting into the taxi, and will increase depending on the number of passengers in your party, not already in the taxi or getting in later time of day night is significantly more expensive and location going to or from a nice part of Managua may cost you a little more due to lowered bargaining power. The cheapest fare for one passenger is C$20 2009, but the same route if you are a party of two may be C$30. A trip all the way across Managua during the day should not be more than about C$50-60 if not coming from or going to the airport. Tipping is not expected though always welcomed.You can also split the cost of taxi to get to destinations that are close to Managua by like Masaya, if you should prefer to travel with modicum of comfort.
There have been increasing incidents of taxi crime in Managua. The most typical scenario is that an additional passengers enters the cab just a short distance from your pickup, they and the taxi driver take you in circles around town, take everything on you, and leave you in a random location typically far from where you were going. Check that the taxi has the license number painted on the side, that the taxi sign is on the roof, the light is on inside the taxi, and that the taxi operator license is clearly visible in the front seat. You may want to make a scene of having a friend seeing you off and writing down the license number. Care should be taken especially at night, when it may be best to have your hotel arrange a taxi.
Hitchhiking is common in more rural areas and small towns, but not recommended in Managua. Nicaraguans themselves usually only travel in the backs of trucks, not inside of a vehicle they are traveling with a group of people 3 or more. Some drivers may ask for a little money for bringing you along - Nicaraguans see this as being cheap, but will usually pay the small amount US$1/person.
Bus is definitely the main mode of travel in Nicaragua, and a great way to get to know the country's geography, people and even some culture music, snack food, dress, manners. Most of the buses are old decommissioned yellow US school buses though often fantastically repainted and redecorated. Expect these buses to be packed full, and your luggage if large may be stored at the back or on the top of the bus along with bicycles and other large items. You'd better be quick or you may be standing most of the trip or sitting on a bag of beans. Some have not replaced the original seats meant to carry 7 year olds, so you may have sore knees by the end of the trip. People often sell snacks and drinks on the buses or through the windows before they depart or at quick stops. A typical fare may vary between US$1 or less for short ~30min trips to US$3-4 for longer trips. Most cities in Nicaragua have one main bus terminal for long distance buses. Managua has numerous terminals, each serving a different region of the country depending upon its geographic placement in Managua. Mercado Israel Levites, in the western part of the city, serves cities on the Pacific Coast to the north, e.g. Leon, Chinandega and all points in between. Mercado Mayoreo on the eastern side of the city serves points east and north, like Matagalpa and Rama. Mercado Huembes in the southern part of Managua serves points south, like Rivas/San Jorge and PeÃ±as Blancas.
Another method of traveling cross country are minibuses "microbuses" as they are called. These are essentially vans, holding up to 15 people some may be larger, shuttle sized. Minibuses have regular routes between Managua and frequently travel to relatively nearby cities like Granada, Leon, Masaya, Jinotepe and Chinandega. Most of these leave from and return to the small roadside microbus terminal accross the street from the Universidad Centoamericana and thus the buses and terminal are known as "los microbuses de la UCA". Microbuses run all day into the late afternoon/early evening depending on destination, with shorter hours on Sunday, and a definite rush hour during the week as they service nearby cities from which many people commute to Managua. The microbuses cost a little more than the school buses, but are faster, making fewer stops. As with the school buses, expect these to be packed, arguably with even less space as drivers often pack more people than the vehicle was designed to handle. On the other hand, most drivers and driver's helpers are friendly and helpful, and will help you store your baggage. Microbuses cost a bit more than regular buses. They run to the main bus terminals in Leon and Chinandega, to the Parque Central and Mercado de Artesanias and then leave from another park a couple blocks from there in Masaya, and to/from a park 1 block from the Parque Central in Granada. There is more limited microbus service to other cities out of their respective bus terminals in Managua.