My understanding is that the “baptism” of John is not sacramental baptism in that it did not wash away original sin nor leave a mark on the soul. It was a baptism of repentence - an outward sign if you to turn away from sin and renew your life in anticipation of the Messiah. As Matthew 3:11 says:
I am baptizing you with water, for repentance, but the one who is coming after me is mightier than I. I am not worthy to carry his sandals. He will baptize you with the holy Spirit and fire. Matt 3:11
Since the Apostles were baptizing in the name of the Father, Son and Holy Spirit (different from what John was doing) I think we can say they were not the same baptisms. It is wholly probable that Jesus baptized his disciples either before the resurrection or just after before Pentecost.
In any event, remember that we are bound by the Sacraments but God is not. Interesting question though. I would love to hear from others who have a better knowledge than I.