I've lived in MKE for about 10 years (many of those as a student at Marquette and UWM). Here is what I can say about it:
1. I LOVE Milwaukee. There are amazing people here, activities, festivals, and nightlife spots if you avoid the big trendy stuff.
2. Housing. I've lived in many neighborhoods here. West of the river (Riverwest) is my favorite. It is true that it can be spotty with crime, but if you have some common sense it's no big deal. Like, don't walk alone at night with your headphones on...you'll get mugged. I live in a quiet little pocket of Riverwest that is mostly homeowners. However, the house next to me is 4 units and owned by a slumlord. A couple weeks after I moved in, one of their tenants died there of heroin overdose and the house got shut down and boarded up for 2 years. Now it's back open and the neighbors are once again trashy and obnoxious. This is the kind of thing that happens in Riverwest, but it is a very involved and supportive community, and the good people here really work hard to improve the neighborhood and keep crime down.
If you choose to live closer to campus, there are problems to be had there as well...personally, I think there is more risk of vandalism by the campus. Way more car break-ins over there than in Riverwest. And a lot more noise from the undergrads. BUT, parking at UWM is a bitch, so it's nice to be walking distance. Riverwest is cheaper though.
I did undergrad at Marquette, but I would never choose to live around there. The surrounding neighborhood gets real hood and the crimes more serious. Also ain't shit to do there.
Bayview is lovely, hipster, slightly pretentious. It is affordable, but kind of a hike to UWM. Also, your friends on the east side will never want to come out to Bayview because it's "soooo far" (actually less than 10 min car ride).
3. Bottom line: my vote goes to Riverwest. It's safe if you're not a drunk idiot. If anyone is considering a specific spot in Milwaukee, feel free to message me and I can offer my input on that area.