Most schools have really good equine programs---suggestions would probably depend on what region you want to be in, I suppose. I would ask schools about their faculty, research, case loads, and facilities if you are concerned about how innovative one school is compared to another or if you specifically one good equine repro people.
Otherwise, a specialization in equine therio will probably only become an issue in choosing a vet school for a residency... So you could start 'shopping' for schools then... or now if you want to stay put for the whole experience, I guess.
Another thing to keep in mind is internships and private breeding farm practices after vet school if you don't want to do a residency.
