The problem insects could be whiteflies. They are tiny, white flying insects that fly up to make a cloud when an infested plant is disturbed. You can control these pests through insecticidal soaps, yellow sticky traps, insecticidal oils, or rotenone/pyrethrin mixtures. Yellow sticky traps, that you hang around your plants are available at many garden centers. They are the safest solution, as no chemicals will touch your plants.
If not whiteflies, they might also be leafminers. Leafminers are flying insects that actually embed themselves in the leaves of a tomato plant, which is why they can be so hard to get rid of. Although these bugs do not kill the tomatoes, they do hinder the growth because they cause damage to the plant's leaves, which interrupts the photosynthesis that allows the tomato plant to thrive. You can use the same remedies suggested for whiteflies.