these things suck from the bottom of the leaves right? thats always a PITA to deal with.
if you are not aversed to chemicals, you could just bomb them with a systemic like imidicloprid. i personaly dont care, and have eaten plenty of toms that were subject to a blast of imidicloprid. just use as directed. i think they want you to wait 3 weeks before harvesting.
you could also just spray frequently. im guessing the flys themselves are the ones that reproduce. id bet you could kill the flys themselves with some sort of insecticide and prevent them from reproduceing. u just need to find out how long it takes from them to become flys to becomeing sexually active... and spray at a shorter interval.
you could also try something like abamectin. i use it to kill mites, and apparently its classed as a "trans laminar" pesticide meaning it will diffuse throughout the leaf and not simply lay on the surface. epro is complicated to apply tho, you need to ph some distilled water to 5 then add some surfactant so it dosent bead up and instead clings to the leaf in more of a filmlike mannor.