JFK is also a preferable location for staging supersonic flight because you don’t need to pass over/near a massive population center on a route to northern Europe
A plane like Boom that doesn't use afterburners could take off from any airport as long as they stay subsonic over populated areas.
I don't know what Boom's expected runway requirements are, but if they're anything like the Concorde's (>11000ft), there's no way they'll actually be able to take off from LGA.
Edit: At least one source says that Boom's plane requires no less than 10000ft[1].
[1]: https://www.aviationtoday.com/2018/11/13/aerion-boom-taking-...