Strategies to reduce EMF radiation
It seems to me that you need magnetic shielding if the electron microscope is affected.  Here's what I would try:


Use your gaussmeter to determine if the source of the magnetic is actually the power line.  5 milligauss seems like a lot if you are any distance away, because if the power cable contains all three phases, the net current in the cable should be near zero.  The magnetic field contributions from the three phases should cancel each other if you are a reasonable distance away.  It can be checked by measuring the field as you get closer to the power line; the field strength should be inversely proportional to the distance from the cable if the cable is the source of your field.
If the cable is not your source, look at areas where the three conductors are not close together (junction boxes, switches, etc).  Any individual conductor separated from the other conductor forms a loop which will produce a large local magnetic field.  Your gaussmeter will help you check for these also.  If possible, move these.  If the power conductors are run on separate wires, have them bundled together.
Check your furniture and structural fixtures.  Steel structures, tables, etc can distort and locally concentrate the magnetic field in an area.  Once again, your gaussmeter can help you here.
If the power cable is your problem and the three conductors are close together, I would try buying some highly permeable magnetic shielding conduit (something like MuMetal).  It is normally used to shield the cable from outside influences, and I have never tried using it in this manner.  You could probably have a cable tray with a cover fabricated but I know there are manufacturers that provide flexible conduit.  For this to work, you don't need to sheath the entire cable, just the length near your measurement for some distance in each direction.  You can get a short length and use your gaussmeter to see if the field is attenuated, then make the decision whether to try it.