I live out in West Roxbury (8 miles from the city) and it takes me about 20-45 minutes to get in during rush hour but I have a four bedroom/ 2 bath place for $2200. In town you will pay $2200 for a 1 bedroom.
Avoid the realtors as you will be 1/2 to 1 months rent as a "fee" to them. Horrible, but I paid 1/2 month and the landlord paid the other 1/2 to get into a nicer place.
More dangerous neighborhoods are Dorchester, Roxbury, and Mattapan, but the prices are considerably cheaper. Try Malden, Somerville, West Roxbury, Roslindale and Quincy for safer and cheaper neighborhoods.