The first two times I rode the BNY5B I drove from my parents house in Ridgewood to Jersey City and took the ferry from Harborside. Nice way to start the day. Then the Harborside dock was redeveloped out of existence and the schedule from any of the other ports didn't get me to the start in time. My last two years, and for the NY100, I just drove across the GW and down Riverside to around 122nd St. Plenty of free street parking that time of morning, and I get a nice 10 mile warmup ride down the Greenway.

You might want to check with the ferry company. They've had BNY5B special runs, but they usually don't announce it until a couple of weeks before the event.