Hi,
Tomato seeds will be fertile. Peppers need to be completely ripe(not green) to have viable seeds.
The real question is though, will the seeds grow plants true to the original veggie I bought. With peppers, they will probably vary from the parent since peppers cross pollinate so readily. Tomatoes don't cross pollinate as easily, but you need to know whether or not the farmer grew a hybrid. Hybrid tomatoes won't grow true.
Of course if you don't mind getting variation, then it will be fine.
Remy