Huge distances can be travelled easiest by plane of course. Additional advantage is that you even get to skip the rather chaotic customs clearance at borders if you fly between Central American countries. But obviously, you also miss out on the sights, sounds and smells of slowly traveling by bus.
Within Mexico most huge cities have airports. Especially Guadalajara, Mexico City and Cancun have lots of international connections. AeroMex is market leader, but Volaris has a lot of good domestic and international deals as well.
In other Central American countries, only the capitals usually have a proper airport. Beyond that, you either have to take the bus, or if you are lucky you can take a small plane. A good example of the latter is the trip from Managua (Nicaragua) to the Corn Islands in front of the Caribbean coast.
Long-distance buses are by far the best option in both Mexico and Costa Rica. These are usually well-equipped, with TV screens and toilets, and are not too expensive (though much more expensive than in most of Central America). They are also a good way to cross borders: we took one from San Salvador (in El Salvador) to Leon in Nicaragua, traversing Honduras in between. And from Rivas (Nicaragua), but also from Managua,there are several direct buses going to and from Costa Rica.
Finding out which buses to take is quite a task. In Mexico, several bus companies serve different areas of the country, though they do overlap partly. Some of the bus companies:
- Flecha Roja / Flecha Amarilla: has lots of buses in the regions north of Mexico City
- Primera Plus: luxury coaches. They serve the longer distances from for example Mexico City to Guadalajara, Queretaro and Guanajuato
- TF Frontera: they serve regions in the north from Mexico City
- ADO Bus: they seem to almost have a monopoly in the south, along the Pacific coast and towards Oaxaca, Tuxtla Gutierrez and San Cristobal de las Casas
As said, there are many many more companies, depending on the region. https://mexicoautobuses.com/ gives you a good overview, though often the official sites don’t have all the lines. Best is to find out the times and connections by going to the terminal if you have time
In the other Central American countries, it is even more difficult to navigate your way around. Most of the transport between cities and villages happens in so-called chicken buses (link): slow, affordable transport with lots of local flavor. An absolutely unmissable institution is Centro Coasting which has lots of information about connections and timetables.
Even smaller are tourist vans that are running in certain parts of Central America. Www.monte-verdetours.com for example has a van (max 15 people) going from San Cristobal de las Casas in Mexico to several cities in Guatemala. And Gekko Trails Explorer offers convenient connections between the main tourist hotspots in the various countries, for very reasonable prices.
Driving by car is obviously possible as well. Most roads in Mexico are well-maintained. When you get further to the south, beware of the speed ramps you will encounter every couple of hundred metres. These babies are no joke.
Going further south, road quality sometimes becomes an issue. In general though, most roads are at least decent. In Costa Rica, it being the richest country of the region, the situation is even better.
Train travel is almost non-existent in all these countries, even in Mexico. A boat is only an interesting option between La Union (in El Salvador) and Nicaragua. It is rather expensive (apparently around 50 dollars pp), but it only takes around two hours and you avoid Honduras entirely.