yale is not in a very unsafe area. While it is true that new haven is not the best, there is a separate part of the city called Yale-New Haven and that is entirely different. I should know-- I did my undergraduate degree there. There is not a lot of muggings and crime on campus. As far as theft goes, I would not leave my lap top unattended in any college. In addition, all the dorms have swipe cards to get in and out of. My father, a very overprotective Italian dad, born and raised in NYC, tried to break into the buildings to make sure it was safe. If he could not get in, we were all satisfied.
If you can, I would also recommend trying to get in with one of the residential colleges (kind of the equivalent of dorms) for the undergrads and being a fellow (where you get room and board). These positions are hard to get but well worth it.
If anything, the apartment complexes are in a less safe area than the dorm. Harkness is beautiful and really centrally located to most of campus.