You can get around the air intake problem by adding a snorkel. Military Humvees often have a snorkel attached, and it allows them to submerge in up to 5 feet (1.6 meters) of water (see this page for some nice pictures of a typical snorkel). In order to handle submersion like this the engine and the rest of the vehicle must be waterproofed. So your question changes into, "Is it easier to waterproof a diesel engine than it is to waterproof a gasoline engine?"
To waterproof any off-road vehicle, there are lots of different things to think about. For example:
- Any electrical devices like the instruments, engine control computers, motors (for fans, windshield wipers, etc.), lights, battery, etc. must be sealed.
- Any venting for things like the crankcase, differential, etc. must be sealed (or vented at the same level as the snorkel).
- The fuel tank must be sealed and vented appropriately.
- Any chamber or crevice that can fill with water must have a drain.
In general, it is easier to waterproof a diesel engine than it is to waterproof a gasoline engine because of the sparkplugs and ignition system in a gasoline engine. These components run at high voltage and sealing them is harder (but not impossible). A diesel engine, on the other hand, has no ignition system (see How a Diesel Engine Works). If the diesel engine has a mechanical fuel pump for the injectors and a mechanical transmission, there are also no engine control electronics to worry about. These features can make a diesel engine relatively easy to waterproof. That's why most military vehicles that ford rivers or run submerged have diesel engines.
Here is an interesting link:

