LGA doesn't allow any flights from more than 1,500 miles[^0], so has to be either JFK or EWR.
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-...