There are quite a lot of reasons for this, but it's a complicated design environment, and that's why it's not always the case.
Seals and cooling
The inside of a plane's wings is the same fluid as the air around it, but the inside of a boat's hull is a different phase than the water outside. Basically you can never have a rotating shaft over a pressure difference that doesn't permit some fluid through, around the shaft. There are ways to mask this, so that no one ever sees water leaking into the hull. For instance, you can have an intermediate stage between the hull and the water where air is pumped into a higher pressure cavity. Then it's possible that the seal can bubble with air passing out into the water.
Whichever design the ship maker uses you can't change the physical fact that you'll have some fluid flow through the prop seals, be that air or water. This presents a good reason to have the prop on the back of boats and the front of planes. Pressure is higher at the front because of the kinetic pressure of the fluid, and lower at the back for the reverse reason. By putting the prop of a boat in the back you reduce the pressure difference that the seals have to deal with. The plane has no such concern, and might prefer more air pressure and flow around its engines for cooling. In fact, Wikipedia seems to agree with the cooling point for plane engines.
In pusher configuration, the propeller does not contribute airflow over the engine or radiator. Some aviation engines have experienced cooling problems when used as pushers.[33] To counter this, auxiliary fans may be installed, adding additional weight.
Stability
A moving boat or plane has an aerodynamic center of pressure. If this point is behind the point of thrust, then it's a more stable setup and if it's in front then it's a less stable setup. It's likely not a problem either way because there are other dynamical factors that make it stable, or you have a pilot that acts as an active control system.
Nonetheless, planes worry about stability a lot more than boats.
Operational considerations
As others have pointed out, boats logically don't want the prop in the front because you're more likely to hit something (like a sandbar) with the front of the boat, and you don't want to shred things. This quite possibly dwarfs the basic physical considerations.
In fact, as I was thinking about cavitation concerns, it seems clear that the back of the boat isn't the ideal place. Directly under the hull would be superior. But this a) doesn't give a direct shaft line to the engine and b) it could make the prop hit the ground or a whale. For this case, it's clear that the operational safety concerns are much more pressing than a little bit more performance.
A propeller imparts momentum on the air - when the blades hit the air molecules, it gives them momentum towards the back (high pressure) side; this creates a net velocity towards the rear of the propeller. Normally air molecules in the plane of the propeller have equal probability of moving forward or backwards; the propeller's action makes the situation asymmetrical. Since more air molecules move backwards, a low pressure area is created in front - and air will be pushed towards this region be the atmospheric pressure "far away".
Best Answer
You are correct if your boat will only travel in a straight line.
In real life the motion of the boat will often have a yaw angle, so that it is moving slightly "sideways" relative to the water. For example it is impossible to make a turn and avoid this situation.
If the front is too sharp, the result will be that the flow can not "get round the sharp corner" to flow along both sides of the boat, without creating a lot of turbulence and waves which increase the drag on the boat.