In the early days of rotorcraft development, the machines that flew then did indeed have a distinct difference in altitude between the left and right sides. The left side of the aircraft, at a hover, was considerably lower than the right side. Therefore it was determined that the right side should be the pilot's seat. If the rotor system turned in the oposite direction the effect would be reversed.

Generally, technical reasons choose the pilot seat.
Have a look at the Robinson R22, due to the rotation of its blades, it would fly inclined on the left .

The right blade is the fastest one when flying : it speed is the rotation speed plus translation speed

The left have it speed equal to : rotation speed minus the translation speed.

Also the fuel tank is on the left side. So, the pilot has to be on the right side to equilibrate the system. On a big helicopter, this effect is minored, but on a light one as a R22, it so important that the helicopter could not fly.

Other reason that the pilot position is on the right is because the pilot needs his right hand to fly the A/C. Since the collective doesnt need the attention that the cyclic needs its only natural to put the pilot on the right hand side, thus leaving the left hand to tune radios and perform other tasks.

another very simple and logical answer: in earlier helicopter models, and in most of today's smaller models, having the collective stick on the left side made it awkward for the pilot to enter and exit his seat, having to step over the collective control stick either way. Thus entering and exiting from the right side made more sense. Plus, it simplified the collective control linkage system.