Rather than the fly kind of leaf miners that attack tomatoes, which seem more prevalent in the south, my garden - also in NJ - is beset by the moth kind. I get different kind of leaf miners that go after my aquilegia and maybe yet another or same that go after the lambs quarters and related plants.
Rather than squiggly tunnels, the tomato leafminer caterpillars make pockets between the top and bottom layers of tomato leaves. Thin windowpane layer on top and bottom with a dark bulge where the caterpilllar is hiding, and dark green/black deposit where they left poop behind.
The adult moths are non-description tan and small -- maybe a bit like sodworm moths and pantry moths. They normally don't overwinter well outside here -- only during very mild winter. They are more likely to have survived in the house or were brought home with groceries or greenhouse garden plants. One year, I lost control of them when I brought them in with some mature and fall-started tomato plants for the winter indoor garden, then they managed to use my winter indoor garden to perpetuate several generation over the winter, then moved outside with the plants to infest my summer garden.
There is another one called tomato pinworms. I forgot because I only learned about them recently thanks to another member who posted about them. I get those sometimes too.
...the big black fly is probably blowfly which is the earliest big flies (they have suction pads on their feet) -- I once worked at a scientific laboratory where the research assistants set out traps to CATCH them in early spring, when air was still a bit chilly like now, so they could perform brain surgery on them (true story) ... or they could be tachnid flies if very hairy.