When in lived in Boston with my girl for about a year I had absolutely no problem up there. Boston is always considered racist but Massachusetts did elect the first black governor largely due to the Boston metro area. So Boston is no more racist than any other big city, they have just got a bad reputation in the past and it stuck.
It is a very segregated city though. While New York isn't perfect by all means, is city truly is a melting pot with all races living side by side and in the same neighborhoods. Boston however, has the Irish living one side, the Italians living on another side, and blacks and asians living all the way on another side. The only truly diverse neighborhoods are near Harvard and Boston College. Even in the south, racist rednecks live right next door to black people. Something is wrong in your city dude.
But is it really Boston that is special? Most big cities to this day are still segregated. I think one of the only things that really set Boston apart is the fact that it is one of the only big cities in that has majority of white residents. I'm not from Boston I only lived there for a year. Baltimore is where I was born and raised.
Chicago is a pretty segregated city as well and also has it's own problems with race like Boston, albeit, to a lesser extent. I'll never forget when i visited Chicago two years ago, i took a bus to go see the United Center and figured i was in the black part of town when all the white people got off the bus and black folk started getting on.