I would first consider changing the clothing worn with the waders or nippers. Cotton does a very poor job of wicking moisture away from the skin. Dry skin stays warmer. Much better to have a material that wicks moisture away from the skin. There all all sorts of thermal undergarments that come in light, medium, and heavy weight styles designed for skiing, fishing, and other cold weather sports that can be worn under a light weight pair of pants made from synthetic materials such as the styles with zip off legs. Ditching the cotton jeans just might be the answer. I use REI Power Dry bottoms and REI Sahara pants but there are many other similar products. If that is not warm enough I add a pair of fleece pants.
Breathable bootfoot waders are hard to find. Most anglers have gone away from neoprene in favor of breathable materials. But Cabelas and Bass Pro sell bootfoot neoprene chest waders for around $200. On both websites search fur hunting waders as you won't find these in the fishing sections. And I would still recommend against wearing cotton under neoprene waders.