I have been commuting by bike from my home to a train station in sub-rural New Jersey for six or seven years, and two years ago started using a folding bike so I could ride in NYC as well. In that time I have had my wife drive me to the station maybe ten times on account of inclement weather, and I've stayed home on account of weather on another ten occasions; otherwise I have used only the bicycle and the train for getting to work. My commute is now about 16 miles of bicycling every day, plus another 90 or so on the train.
In that time...
--I have been in one accident which drew blood, when I rammed a taxi door as it opened. Scared the **** out of some unfortunate tourist, to whom I apologized profusely, but she was mostly concerned about the blood coming from my cut knuckle. My fault, obviously.
--I have been in one accident that required hospitalization, but it doesn't count, because I wasn't on my bike at the time. My train derailed and about six people went to the emergency room. I was not among them.
--I have had three close calls in which I almost hit taxis who swerved in front of me and then slowed down. Would have been my fault; it's what taxis do, you have to expect that.
--I had a very close call in which I was almost hit by a car running a red light. That was scary. I have had two similar close calls in which I was almost hit by cars making legal left turns (tho without turn signals).
--I have yelled at about five people on account of various transgressions; on three occasions I was sufficiently polite about it that they actually apologized with some sincerity.
--pedestrians have yelled at me on two occasions, probably with some justification.
--I came within inches of running over a squirrel once. It was running from a mockingbird, which I may also have hit --it seemed to fly right through my spokes-- probably an optical illusion.
--I have been hit by one goose, and had narrow misses with that or other geese on two occasions; and once I was almost run over by a deer. The goose, by the way, attacked me without provocation, warning, or any realistic idea of what it was going to do to me; and it never apologized. Luckily it kept its head out of the spokes. My policy now is to yell at geese as early and as loud as possible, but it doesn't seem to help.

That's all the bad news I can remember; the rest is just sunshine, tailwinds, and the occasional glorious moment like the view from the bicycle lane on the Brooklyn Bridge. No thrown objects have hit me, and I haven't noticed any that missed me. In my experience 99% of drivers are courteous and cautious. NYC drivers are more polite to bicyclists than NJ drivers. NYC bicyclists are horrible, they have no courtesy and no caution. Given the number of miles, I'd say the train is marginally safer than the bicycle, but that may just be anecdotal evidence.

Rudi