The trip takes two days and should not be undertaken without adequate preparation. Hiring a guide will prevent you getting lost and may provide some measure of protection against bandits who have been known to operate in this area. Although there are no regular passenger ships to or from Honduras, it's often possible to arrange passage with a fishing or cargo vessel if you pay your way. Negotiate directly with the captain. On the Pacific coast, try San Lorenzo to find boats to Nicaragua or El Salvador.
Trains are slow, rudimentary and very cheap.
Services have been disrupted in the past, so check whether the trains are actually running before planning to use one. Boats are common modes of transport between the Bay Islands and along the Caribbean coast, especially in Mosquitia, where there's just one road. There are plenty of taxis in most towns but they are not metered, so negotiate a fare before you get in. Car rental is available in main towns and the main roads offer excellent driving. Hitching is generally easy in rural areas, where trucks often stop to pick up passengers.