In my experience, pests attack shaded plants a lot more than plants in full sun. So, giving them plenty of sunlight will probably help.
Making sure they have enough (not too much) potassium, calcium and silica should also help to increase the insect and disease resistance. Make sure the nitrogen is balanced with the potassium and probably the calcium levels, too. If you get too much nitrogen, the potassium probably won't do its job well. If you get too little nitrogen and too much potassium/calcium, the plant will grow slowly and if severe, may actually be more susceptible to disease.
Some kinds of aphids are a much bigger problem than others. Some can devastate peppers, I've found (and some hardly touch them). I had some that blew in with the wind on our Ethiopian eggplants last year (but after we tried dousing the eggplants with cayenne, they spread to the peppers, too). They were large, fast, armored aphids that bred really, really fast and wouldn't let the peppers grow. When I fertilized with a foliar spray of calcium nitrate, they didn't like the peppers so much anymore (but the ladybugs, which came and ate the remaining aphids, didn't mind). I imagine a foliar spray of sea minerals might repel pests (since they're salty, and these pests like juice; they might dehydrate with the spray concentrated on the leaves). I haven't tried it, yet (just in the soil, which peppers like), but it's a hypothesis. Sea minerals in the soil did strengthen my indoor potted pepper against its spider mites infestation, and it did eliminate a fungal infection it was suffering from. It didn't eliminate the spider mites, though, unfortunately (but they're not as much of a problem).
As far as aphids on tomatoes go, we only had black, winged aphids on them, and not in large numbers (they weren't a big problem).
Some people talk about using cayenne against aphids, and although it works temporarily, if the aphids are bad, they'll probably bounce back from it with a stronger taste for peppers. Diatomaceous earth might help to control them, but not to get rid of them.
You might consider growing Solanum galapagense, which is supposed to have whitefly resistance. Whiteflies don't bother my tomatoes terribly, though. They seem to prefer other plants in the area (including grapes, Ethiopian eggplant, and peppers, especially the Early Jalapeños we grew).