As pointed out, optical identification of the fleets is effectively impossible unless we postulate improbably large space telescopes, with mirrors measured in kilometres rather than metres.
However, visual identification of targets isn't the only way to go, and even visual identification might be useful if we are looking at something else.
Space is both a vacuum and extremely cold, so the heat energy of the spacecraft stands out like a beacon against the background of space, and isn't absorbed by intervening fluids (at least not on the scale of the solar system. There are interstellar nebula of gasses and dust which can absorb energy on a cosmic scale). This is the reason there is "no stealth" in space, the spacecraft are highly visible in the infrared spectrum.
This includes heat radiating from the ships even when they are drifting, since a great deal of "hotel" power in needed for life support, running the various ships systems and so on. Unless the aliens live in a cryogenic environment, the ships will have to be at several hundred degrees Kelvin just so the crews can survive.
The radiated energy of the ships is compounded when they use their engines. Atomic Rockets points out that the Space Shuttle engines put out enough energy that the small manoeuvring thrusters could be theoretically detected out to the asteroid belt, and the burn of the SSME would be visible from the orbit of Neptune. More detail can be found here.
Exhaust plume of an F-35
So while the ships are still smaller than a single pixel, you will have a large and otherwise inexplicable infrared source in deep space. Assuming you have other information about the aliens, you might be able to determine who is who by carefully looking at the infrared signatures. One set of aliens might have significantly warmer or cooler spacecraft because of their environmental preferences, and the energy used to manoeuvre will be very distinctive, especially if you have information about the actual sizes/masses of the ships (larger ships will require more energy to move, so you have a metric of sorts to determine which fleet is which).
Other sensors are available as well. We use radar on Earth, and the Arecibo radio telescope has been used to do radar scans of Venus, providing surface details even from that distance. The sensitivity of the telescope was great enough that during the Cold War it was used for Electronic Intelligence (ELINT), analyzing Russian radars by gathering reflections from the Moon! With this level of sensitivity, radar imaging of the fleets is also possible, but once again, you would have difficulty resolving individual ships.
Arecibo radio telescope
Even more exotic systems could be postulated using current technology. A satellite could be launched with a high powered laser to conduct LIDAR scans of the fleets, to compliment optical, infrared and radar searches. This would likely be in support of fine tuning any observations, and aiming the hypothetical super weapon in the OP. Neutrino detectors deep beneath the Earths surface could also be used to attempt to detect the neutrino emissions from the ships nuclear reactors, although this would be a very low resolution detector.
So although visual detection would not be possible or readable at this time, there are still multiple systems which could be used to locate and identify the various fleets.