What program are you using?
In Simplify 3D you can adjust fan speed. You might be able to in the MakerBot software that comes with it but I'm not sure.
Also if it is a PSU issue that can happen when the extruder is heating and using more power and a failing PSU can't keep up.
It could be the fan itself is dying also.

Also one last thing. Make sure the outlet you are using that nothing else is on the same breaker. If an AC unit or something else that turns on and off can make weird changes where you notice it fluctuates.