There are several options to go all around Nicaragua.

You can choose different shuttles services like, NicaRoads, Paxeos, Adelante express, iskatravel, .  They  run between diferent destinations, are reliable companies and the prices are not expensive more if you travelling alone.

Public busses… That will be the cheapest option. They run frequently, are not comfortable cause the most they put inside better for them even in the middle, they are always delay and there is good possibility they broke town at the middle of the road, but is a funny ride if you have the time, For more detail info you can ask at the forum.

Also, you can check the following bus schedules site: (added by Mike @ Farmstay El Portón Verde)

Flying in Nicaragua you have to use small regional Planes as la Costeña.  La costeña flies to Bluefields, Corn Island, San Carlos and Puerto cabezas. The airlines have a baggage allowance of approximately 22 pounds per person.

Hiring a taxi

Taxi Managua This is secure and reliable transportation but not cheap

Sometimes driving in a place that you don´t know is a bit difficult, so some people rather hire a taxi, taxis are abundant, but is a bit difficult to know which one is pirate or not, taxis in Nicaragua don´t have an specific color and many can have the taxi sign on top but the ones that are not pirates are the ones that has a red/white/red license plate. All others are illegal and are probably not insured or safety inspected on a regular basis.