As part of normal procedure, it was searched by security teams using sniffer dogs before it took off.
The plane, a Pakistan International Airlines (PIA) flight, was on a scheduled flight from the US to Pakistan with a stopover in the UK.
As part of normal procedure, it was searched by security teams using sniffer dogs before it took off.
However, as the plane was preparing to leave JFK international airport at 2100 local time (0100 GMT), a bomb threat was received by telephone.
The caller had said there were three bombs on board, which would detonate on take-off.
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The pilot decided to take off anyway, but then turned back over Boston so the plane could be re-examined.
It returned safely to JFK, and was moved to a remote part of the airport.
General Musharraf was taken to the VIP lounge.
"We have no reason to believe that there was a bomb on this plane," airport spokesman Alan Hicks said.
The plane was reported to have been allowed to depart again early on Thursday morning.
General Musharraf was in New York for the UN Millennium Summit, which he addressed last week.
Making his first appearance before the UN General Assembly, he raised the long-standing Kashmir dispute with India.
General Musharraf said Kashmir was the root cause of tension in South Asia and accused India of intransigence in resolving the issue peacefully.
General Musharraf assumed power in a military coup last October.
After the takeover, former prime minister Nawaz Sharif was put on trial, accused of trying to divert a flight from Sri Lanka which was carrying General Musharraf.
Mr Sharif was subsequently jailed for life for hijacking and treason.