The bottom two threaded holes are for those who wish to install a rear peep sight. The hole above it is NOT supposed to be threaded. That is where the shaft from the ejector, which is located inside of the receiver protrudes through.
You should probably do some research on field stripping the Marlin levergun. To properly break it down for cleaning, you remove the lever hinge screw, drop out the lever, remove the bolt, and with a pair of tweezers lift out the ejector. You can then clean the rifle in the same fashion that you would a bolt action rifle, from the breach end.