Yes, certainly the Trinity was present, and Jesus’ baptism is one of the events we point to when demonstrating the existence of the three Persons, but the question was whether the Trinitarian Formula was used.
Unless God chose to reveal the Trinity to John at that moment and inspire him with the words (and we have no indication of that), it would seem that John could not have used the formula, since the Trinity was unrevealed and Jesus did not command baptism in the name of the Trinity until nearly the end of His ministry, after John’s death.
As others have said, Jesus’ baptism was not a Christian baptism, and nor were any of the other baptisms performed by John. As with marriage, Jesus took a pre-existing rite (Jewish ritual washing, and specifically the variation practiced by His forerunner John) and raised it to the status of a sacrament.
Since Jesus gave the Great Commission and commanded us to baptize “in the name of the Father and of the Son and of the Holy Spirit,” that has been the required form of the sacrament. Before that, the sacrament as such did not exist. (Well, it’s possible that some of the baptisms the Apostles did while Jesus was alive were Christian baptisms, but we’re only told about Jesus giving us the proper form near the end of His ministry.)
It’s possible that the Twelve and Jesus’ other early followers were never baptized in the familiar way and received their regeneration extra-sacramentally from Jesus. (We know Paul was baptized a Christian, but nothing is said about the original Apostles except that they performed a few baptisms.) Then again, maybe He baptized them Himself or had them baptize each other. The Scriptures do not tell us.