Did you try cleaning the fans? A good brush and some compressed air in the right spots usually can make fans run much better, and some oil.
That external fan is a neat idea, computer fans these days are quite nice and would work perfectly with that setup. there are special low noise and vibration models that also move lots of air.
Also I recently noticed that my enlarger power supply was causing a slight vibration on the table whenever I turned on the enlarger lamp. You could feel it when I hit the footswitch, the metal box of the power supply would pop a bit. So now I have everything off my enlarger table besides the enlarger, the power supply is on a separate box and the timer is wall mounted with foot switch.