There is definitely overlap and both words would probably be ok in your case. A 'plant' is more general. Common types of plants are assembly plants, production plants, manufacturing plants etc. A factory is a type of plant, and it would be the preferred word for the case where there is only one type of item being produced in high numbers (e.g. a ball bearing factory or a tire factory). You couldn't use 'factory' if there were no physical product, or if the work were essentially chemical rather than mechanical. 'Factory' seems to fit your case. On the other hand, if there is engineering, design, and testing onsite, a more general word could be better.