The Mets didn’t boo back, per se. They “booed” (metaphorically, with a disapproving hand gesture — although not that disapproving hand gesture) because the fans didn’t boo, didn’t have something to boo about in that particular moment. As Javy Báez explained, and as he and his teammates demonstrated on Sunday, if the fans boo when the team struggles, the players will boo when they succeed.
(Or at least, they did for a few weeks, until the explanation around their not very new but rarely necessary celebration was made public, and in response was roundly renounced by the organization as part of an ongoing inability to manage the message.