When it comes to the nutrition of navy beans versus black beans, go with the latter if the taste works for the recipe. Why is that? Because black beans are a significantly greater source of antioxidants. When raw, they have an ORAC that is nearly 4.5 times higher than navy beans. When cooked, whether its baked or boiled, the value will decrease substantially for both types, however the black will still have much more. The reason for this is its dark pigments which contain the 3 potent anthocyanin flavonoids: delphinidin, malvidin, and petunidin. On the other hand navy, being almost white in color, have very little. However when it comes to other nutrients such as protein, calories, and minerals, the two are fairly comparable.
ORAC Source
USDA Database for the Oxygen Radical Absorbance Capacity (ORAC) of Selected Foods, Release 2 - Prepared by Nutrient Data Laboratory, Beltsville Human Nutrition Research Center (BHNRC), Agricultural Research Service (ARS), U.S. Department of Agriculture (USDA) - May 2010