Hello and thanks for all the replies!
From what you are writing i can see one major problem with this trip; The luggage situation. I am bringing a light weight road bike without any possibilities for carrying any panniers so Its crucial that I find a way to transport the luggage. I will just be travelling with a light backpack with a spare set of clothes, some long sleeves, tools, some food etc etc.
My girlfriend (which is taking some courses at boston university) is checking out the possibilities by mailing it (prices etc. etc). (Both students on a budget)
I want to be in boston by the weekend and my flight lands in new-ark on the 10th.
I have been on a couple of hilly trips earlier, f.ex through the swiss alps from munich-venice and I like ascents and descents so that is just a bonus i think.
Regarding the safety:
I have never been travelling through a big a city as new york, so the whole thing about bad neighborhoods etc is all new to me. I can pedal pretty fast but not faster than a bullet. Or a throwing spear. Or an arrow. So if its possible i'd like to follow your recommendations and go through long island and then take the ferry from there.
Based off of the comments I think ill opt for the route from manhattan - long island, then take the ferry to bridgeport, connecticut.
I am checking out ridewithgps.com and ill post updates here about the route. And the luggage situation.
If I cannot afford to ship the luggage my only option is then to go by bus to boston and then eventually go for a touring ride starting there.
Thank you so much for all the information!