It is better to get a B in an AP class then an A in an Honors class, just as it is better to get a B in an Honors class then an A in a College Prep class. When colleges look at your application, they want to know that you are challenging yourself and taking hard classes, because they are essentially looking to see how well you will do in their school. AP classes are considered to be tougher then Honors classes, because AP classes are introductory college classes that are taken during high school- that's why some colleges give credit for a high enough AP test score. However, Honors classes are really just advanced high school classes.
Grade reviews done for college entrance are done in an 'over-all' manner. The amount of honors classes taken will be noted and average GPA. Other classes will be looked at, and also that GPA. Individual classes are very seldom picked out to review grades, unless you are seeking to enter a very specialized field, and have taken many college prep classes in that area as honors classes. Most high schools do not offer enough 'specialized' prep classes for specific college interest.