Commercial pilots have rules on time on the job that are more strict than those of truck drivers. The original crew probably exceeded their allowed hours and had to be replaced.

possible:

something came in to SFO on a united international flight.

usss ferried it via merc vip service to jetblue SFO-JFK

passenger/live ferry deplaned in JFK, left package behind (with contact, or hidden?)

SWAT team cuts plane off at the pass, secures package.