I think the feeding of the stink bugs is leading to a secondary infection,
and it is even possible that they are carrying the disease to the tomatoes.
Stink bugs overwinter in garden trash, in woodpiles, under boards, in heavy
weeds and fall garden cleanup will be part of any control effort.
Very young stink bugs (nymphs) can be controlled with a soap spray, but you
have to find them. Adults can be hard to control with the insecticides
available to home gardeners. Sabadilla is recommended in organic circles
when stinkbugs are a severe problem (which it sounds like they are for you).
Sprinkling the plants in early morning may draw out the stink bugs to make
them easier to hand-pick (according to my organic reference book).