Among the East River tunnels (not the ones at Lower Manhattan), the Broadway (N, R, W) tunnel seems the fastest. Yes, the Queens Blvd line gets some good speeds too, but in the 61st St. tube, you often see R46's hit wailing speeds, it's very fun overall.
As for the 3.5-mile Broad Channel to JFK Airport stretch, the last time I was on a R32, we averaged 41 mph steadily to 'never-never-land' (the sights are so beautiful with the ocean and the uninhabited islands with the airport itself in the background) We barely peaked 45 mph before slowing down for Broad Channel. Yes I agree this portion should be allowed faster speeds given the tracks can handle it.
Speaking of which, there are grating structures between the 2 tracks all along the long portion. What are those for?
DANGER - DO NOT GET OFF MOVING TRAIN