What is the difference between a 4 port and a 6 port and what is the best of the two ?

 

Well, a 6 port engine has 6 intake ports, a 4 port engine has 4.

The 6 ports were all NA engines from the factory. 4 ports prior to 86 were mostly NA, while after 86 they were turbocharged.

Here are some pictures of 4 port irons:
http://www.mazdatrix.com/faq/portintk.htm

Here are some pictures of 6 port irons:
http://www.mazdatrix.com/faq/port6p.htm

There is no "better". It depends on what you want to do with the engine.

There is also likely a pretty good explanation of the 6 port system in the 2nd gen FSM.