I think land. I would say that it is currently the dominant mode of transportation in most countries. It might not be cars, but whether it's cars, bicycles, or walking, it is still land transportation. Yes, airplanes move a lot of people around the world, and yes, shipping is a huge industry, but land transport dominates.
I believe that land transportation will still be dominating hundreds of years from now. I believe that to be true, because I believe that no matter how far into the future you look, people are still going to live relatively close to where they work. Even if a person lives 50 miles away from where they work, land transport is the most effective form of transport. Too much of too many countries do not and will not have water way access to hundreds of locations within a city. So water is out. Air is not likely either, because current road systems are in place. It will cost less to renovate and improve roads than it will cost to add hundreds of runways or helipads to existing cities. Even if that were to happen, people are still going to need some form of ground transport to get those final few miles.
My last reason for believing land transport will remain dominant is energy efficiency. Land transport is a fairly low cost form of transport in terms of energy usage. Water is a fairly dense substance, so pushing a boat through it requires a lot of power; therefore, fuel consumption is high. Aircraft, while in a low friction environment (air) must always work against gravity. That's also a huge fuel consumption burden. That's why the Harrier jet doesn't spend much time in hover mode -- it burns too much fuel. Conversely cars are not working against gravity (driving uphill yes), they are pushing themselves through a low density, low friction fluid (air), and the ground friction is minimized through round wheels (rolling friction is often the lowest form).
According to a CNN report, there could be one billion cars by 2020. This will increase fuel consumption by 60%. So, it is high time we looked at other options to counter this problem. Dual-mode vehicles and fuel cell cars are good options. But these have yet to become mainstream.
Right now seaplanes are used as a means of transport on lakes and remote areas such as Alaskan and Canadian wilderness. They are also used by the tourism industry in places like Mumbai, Auckland, Maldives, Sydney etc. The utility of seaplanes in inter-city travel is being studied.
Next option is using cars for the land portion of the journey and ship or boat for the water portion. E.g. The states of Wisconsin and Michigan are connected by ferry services over Lake Michigan. There are terminals at Milwaukee and Muskegon. The ferry accommodates passengers, their cars, trucks, motor-cycles. This decreases congestion of bridges, journey time and acts as a sort of car-pool.
Monorail is a railway which runs on a track which is elevated. It is one of the best intra-city transport systems, especially in congested cities. The other advantage is that it can run unstaffed. This reduces accidents and fatalities associated with human error. The Tokyo Monorail is one of the busiest in the world. Since monorails are powered by electricity, they are environmentally-friendly.
Research is in full swing and who knows? the future mode of transportation might not be either air, nor water nor road. Teleportation may become a reality.
The pictures are attached here.