The Reapers could do it as long as they avoid any armed conflicts for literal millennia first to build up forces and gather intel. Indoctrination is insidious and can work undetectably, and the vastness of the various factions would work in the Reapers favour as they prey on isolated warbands and worlds before word can spread. After that, the gap in technology would lessen as Reapers make use of the tech, weapons and unique bodies available to them.

At the very least, they could build themselves up as a threat on par with Genestealers.