The way I understand this is very simple. Regardless of the difference in meaning perhaps of the different texts regarding water and spirit birth - I look to see how the apostles interpreted and understood how to be saved. What actions did they take?
We find both water baptism, and spirit baptism in the book of Acts. That answers the question for me. The understanding of the apostles was to baptize in the name of the Lord Jesus, and to receive the spirit. We know this because of
Acts 10:44-48. "for they HEARD them speak with tongues and magnify God".
In my mind, this settles any questions there are. If the apostles baptized in water, and received the spirit through speaking with tongues, how much more simple can it get than to do what they did?