While the topic may seem like it has the easy solution of "don't pull into the box unless you have clearance up front," practically, its not that simple.
I have been on long lines trying to get to the Lincoln or Holland Tunnels, and to avoid blocking the box, I would wait on the other side until I had clearance. The problem is that when my light is red, traffic from the cross-street will turn into the traffic upfront, so I find myself NEVER having clearance before moving up front.
It really is a bet - a careful one taking into account of the pedestrians, cops, and whether or not traffic will move at the right time.