Peppers and tomatoes are both self-fertile, each bloom is self-pollinating, often before the bloom even opens. So the incidence of accidental cross-pollination is very low on both in the normal garden. It is so low that most seed savers don't worry about it. In over 40 years of growing both I have encountered 2 or many 3 cross-pollinated seed plants.

But if you wish to be 100% pure guaranteed for some reason then all you can do is bag the blooms to prevent any accidental crossing and only save seed from those fruit.

Dave

Hi Ryan,
Peppers grown close together will cross pollinate at a much higher rate than tomatoes. They seem to attract pollinators more often. It must be the open blossom. 500' is the recommended distance for them. If you grow 2 varieties very dissimilar in growth/flowering habit, you can save seed. Like one year I grew 'Early Jalapeno' and 'Korean Dark Green'. Early Jalapeno had flowered and was producing fruit by the time Korean Dark Green began flowering.
The tomato crossing rate is very low even when grown in close proximity to each other. There are a few exceptions like the currant tomatoes. Their flower structure is different and it cause more cross pollination.
Remy

You can build a screen box and cover a pepper plant while certain flowers are opening and then tie a ribbon to those ones (so you know which ones to save seeds from) an then do the same to the other plant(s). You only need one box and just 1 pepper of each to save seeds from.