The Siege (1998)
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David Proval. Edit (Coming Soon)
There are two possible answers:
One is that subway service in Brooklyn was suspended completely. For instance, the A train from the Rockaways to Upper Manhattan would bypass all stations inside Brooklyn.
That however, would be greatly inconveniencing to passengers, so more likely, given the shot of soldiers lined up on a station platform when Devereaux is giving his speech, they had soldiers stationed at every station inside the borough, do random searches of passengers and their bags for explosives. Edit (Coming Soon)
Both bus bombings - the paint bombed bus and the bus attacked with real bombs - take their names from the registered number of the bus involved in the incident. When the helicopter is flying over the stopped bus, the number "5287" is painted on the roof, which is the bus's registered number with the MTA, thus the reason it's called the "Bus 87 bombing." Edit (Coming Soon)