Depending on the type of basil you grow, it does best in its own space in full sun(it can get a couple feet tall). It may have been getting too much competition(and too much shade) from the tomatoes to grow very large. I prune the lower leaves of my tomatoes for more air circulation to help prevent fungal diseases. Peppers also need full sun, and some types can also get pretty large. Did you inter-plant peppers last year, and how did they do?
Are you planting in ground, or in containers? The Square Foot Gardening forum may have the information you need. Hope this helps.

Ditto what noinwi said. I pruned some of the lower limbs of my tomato plants and it does seem to help reduce fungal diseases (from soil that gets splashed up on the plant during rain or watering.)

someone just told me to plant carrots under the tomato plants. i think I'm going to try it. i was wondering if I could trim the bottom leaves of the tomato plants to make room for them, so thanks for answering that question!