The transition to middle school can be a tough one for kids, and it's wise of you to be thinking seriously about this decision. You probably already know that with an IEP your son is entitled to the same educational opportunities as any other student; the purpose of the IEP is to ensure that your son gets the accommodations (help) and, if necessary, modifications (changes to assignments) he needs in order to access those opportunities--core educational standards, of course, but also any electives, extracurricular activities, advanced classes, and the like.
When looking at the local school options, then, the first thing I'd keep an eye out for is what the administrators' and teachers' attitudes are when it comes to making sure your son has all the opportunities available. If you get the feeling that the school has a "one size fits all" approach to its students, I'd be wary; what you are looking for is a school where the adults make it clear that they understand that every child is an individual. Ideally, the administrators and teachers your student will come into contact with will focus on what his strengths are at least as much as they focus on his learning disabilities, and communicate their interest in making sure he has their help to do his best work.
Finally, when it comes to middle school in particular, paying attention to the culture of the school--especially for students who are "different" in any way--is vital. Middle school can be challenging for young people, as they start transitioning from childhood to adolescence, and finding their "place" in the social scene is both important and trickier than it used to be. Middle school students are starting to shift their frame of reference from pleasing adults to pleasing their peers, and the pace at which they're doing this can vary greatly. Children who are still oriented towards adults may seem "immature" to their peer group; children who are more oriented to fitting in with their peers can find themselves making decisions that, from the point of view of adults, are poor ones. Even though we as adults tend to think of "how a child is doing in school" as being about grades and academics, middle school students tend to think of it as being about making friends and being able to get along with others.
It's important to keep in mind, then, that an unhappy, stressed, or anxious child is not a child who is in a good place to learn. I'd pay close attention to how the school or program you are considering handles bullying, peer relations, and disciplinary issues: how much of a priority does the school or program place on helping students navigate the "non-academic" aspects of middle school? If your son or daughter will be at a school with peers who are already his friends, that will be a great help; if he or she is going into a school that is different from most of his or her friends, it will be vital to find out how the staff intends to go about helping him or her integrate into their peer group.