I doubt it. Sounds like another one of these myths put forth to make JFK seem like a larger than life god. I really doubt a bomber could penetrate that far into Russian airspace.
The Cuban missile crisis ended when JFK surrendered to the Soviets by giving in to their demands to remove US missile bases from Turkey. This is what the Soviets wanted all along. But the Soviets agreed to take their missiles out of Cuba in exchange for an ex post facto announcement that the US was pulling its nukes out of Turkey. Khruschev simply allowed JFK to wait a little while before making the announcement to save face and so it wouldn't appear we were bowing to Soviet pressure. Make no mistake about it, despite the historical revisionism about how JFK the superhero faced down the Soviets, the Soviets really in the end won this one.
Doesn't sound plausible. The B-58 did once hold the record for distance (8000+ miles, Tokyo to Britain, in 1963), so 2 or 3 could have made the trip. But I doubt they would have been able to outrun the inevitable interceptors the Russians would have launched along the borders to meet the returning B-58's.
Remember, (not that Kennedy couldn't have called Khrushchev on existing lines), the "hot line" was not installed until 1963 as a result of the Cuban Missile Crisis.
But, the biggest issue of implausibility has to be in the idea Kennedy would authorize such an incredibly audacious act when the whole world teetered on the brink of nuclear war. Khrushchev was not one to be taken lightly - perhaps the sight of B-58's over the Kremlin may have pushed him to launch missiles from Cuba or made him back down, but it doesn't sound like a likely bet anyone would have elected to take at such a precarious time.
The more likely story is as follows from
http://www.gwu.edu/~nsarchiv/nsa/cuba_mis_cri/moment.htm
"The second volume of Khrushchev's memoirs (Khrushchev Remembers: The Last Testament), published posthumously in 1974, touched only briefly on the Robert Kennedy-Dobrynin meeting, but included the flat statement (on p. 512) that "President Kennedy said that in exchange for the withdrawl of our missiles, he would remove American missiles from Turkey and Italy," although he described this "pledge" as "symbolic" since the rockets "were already obsolete."
Over the years, many scholars of the Cuban Missile Crisis came strongly to suspect that Robert Kennedy had, in fact, relayed a pledge from his brother to take out the Jupiters from Turkey in exchange for the Soviet removal of nuclear missiles from Cuba, so long as Moscow kept the swap secret; yet senior former Kennedy Administration officials, such as then-National Security Adviser McGeorge Bundy and then-Secretary of State Dean Rusk, continued to insist that RFK had passed on no more than an informal assurance rather than an explicit promise or agreement.
The first authoritative admission on the U.S. side that the Jupiters had actually been part of a "deal" came at a conference in Moscow in January 1989, after glasnost had led Soviet (and then Cuban) former officials to participate in international scholarly efforts to reconstruct and assess the history of the crisis. At that meeting, former Kennedy speechwriter Theodore Sorensen (and the uncredited editor of Thirteen Days) admitted, after prodding from Dobrynin, that he had taken it upon himself to edit out a "very explicit" reference to the inclusion of the Jupiters in the final deal to settle the crisis."
Another good source (no mention of B-58's over the Kremlin) is http://www.coldwar.org/index.html