Say I wanted to go from Managua Airport to Granada, Leon, San Juan Del Sur or some of the more remote areas. What are my options for doing so? Can I reserve any of them from outside of Nicaragua?
There does not seem to be buses or other land transportation options directly from the airport. There are some bus stations in Managua, however.
According to the Lonely Planet and Wikivoyage, there are buses to go from Managua to most cities in Nicaragua, including those you named. There is also a bus schedule website but I have no idea who runs this website or how up-to-date this is.
Now, there are multiple bus stations in Managua : "The most important from a tourist point of view are Mercado Huembes (buses to the west and southwest), Mercado Israel Lewites (buses to the north and northwest) and UCA (minibuses to short distance)".
And you should go from the airport of Managua to one of them. I could not find information on specific public transit options to get there, but there might be some buses, or it should be possible to take a cab, and the city does not look that spread and the airport is not far either according to a map. Local transportation options are listed on Wikivoyage.
For all these routes, I could not find any website to book tickets. I think you will have to figure that when you are there. As with many bus services in many countries, there is no reserved seat or time so you can just show up and take the next bus. I have no idea if there is a bus station counter/booth or if you pay to the driver.