What part of the unit stops working?
Is there any air coming out at all? Is air coming out but it isn't cool?
If the blower just randomly stops and no air is coming out, then it comes back, it is most likely the blower going bad. The copper brushes in there get dirty and worn out; a way you can test this is that when it goes out, hit the back of the blower with a screwdriver or something. You can access the blower by popping off the top cover on the quarter panel cover.
If the air coming out is intermittently cool, first is to check the temperature of the A/C Lines went the air is not cool. You want the low pressure line to be freezing cold, while the high pressure side to be warm/hot to touch. If you look under the bumper, above the tailpipe, you will see the part of the A/C lines that go into the rear unit.,
If the lines aren't the right temp, then you might have a blockage in the A/C System. Then it would be time to check A/C pressures...
If the lines are the right temp, then you might have a problem with your temperature actuator. When the air is warm but and the rear is set to be on cool, have someone put a screwdriver on the actuator, and have them put their ear up to the back of the screwdriver (should be quite a long screwdriver), and then you would swap between heat and A/C on the panel for the rear unit. If the actuator doesn't move or intermittently moves, then it should be replaced.
Hope this helps,
- Joe