Whenever I turn the a/c on in my 99 runner I notice that there is a click that happens avery few seconds and it's coming from the passenger side floor board by the computer.Is it supposed to do that or should I check something.

 

There is a relay for the a/c compressor clutch around that area, that's probably what is clicking. Don't know if it should be doing it every few seconds though. Possibly your system is a bit low and the low pressure switch is causing it to cycle. Maybe try a can of the refill stuff, you can get one with a gauge attached so you can check the pressure. They're about $20 so it's a cheap place to start.

 

I have owned 5 4Runners and a Taco; all have done this. And yes, I use AC a lot here!

 

I don't think its any issue. Mine does it all the time.

 

Just the AC cycling on and off.