What's the best way to break up with my boyfriend in prison?

None of the choices are "the best", and he is going to take it hard no matter how you deliver it. Our advice is to get it over sooner rather than later so that he has time to heal. In person, if he is likely to make a scene this would be the least favorable. On the phone, you only have 15 minutes, and in a letter you can really think about what you want to say. Therefore, we think that the letter will give you the best option for delivering the news in the best light you can say it. On the phone or in-person, the emotions will most likely cause ugly things to be said that can't be taken back.