JFK/EWR/LGA - it's the same congested airspace. Does it really make much of a difference?
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-...