Paul Williams, a British convert to Islam, has another article seeking to cause doubt on the Deity of Christ and the doctrine of the Trinity.
But you left out the context of John 17:3, which is John 17:1-5.
Jesus spoke these things; and lifting up His eyes to heaven, He said, “Father, the hour has come; glorify Your Son, that the Son may glorify You,
2 even as You gave Him authority over all flesh, that to all whom You have given Him, He may give eternal life.
3 This is eternal life, that they may know You, the only true God, and Jesus Christ whom You have sent.
4 I glorified You on the earth, having accomplished the work which You have given Me to do.
5 Now, Father, glorify Me together with Yourself, with the glory which I had with You before the world was. John 17:1-5
Jesus is in His incarnation body on earth, and praying to the Father. This passage is against modalism or Sabellianism or “Jesus only-ism” (denial of the Trinity; and saying that the Father became flesh, and there is only one person of God, rather than one substance in three persons.
From being on earth and praying to the Father in heaven, of course He is going to refer to Him as “the only true God”, since there is only one God. But that does not mean that Jesus the Son and the Holy Spirit are not also God by the same substance, the same essence, the same nature.
Verse 5 shows this:
5 Now, Father, glorify Me together with Yourself, with the glory which I had with You before the world was. John 17:5
Shows the eternality of the Son, the Word.
“In the beginning was the Word, and the Word was with God, and the Word was God.” John 1:1
“In the beginning was the Word” = the eternality into the past of the Word / the Son
“and the Word was with God” = the Son and the Father in personal relationship with one another, spiritually – facing one another in conversation and eternal fellowship.
“and the Word was God” = the Word and the Father have the same nature, but are not the same person.
The Father sent the Son to earth to do the work of the redemption (John 3:16) and John 17:1-5 is all fully compatible with the doctrine of the Trinity, and in fact, understood properly, actually teaches and proves the doctrine of the Trinity came from the Bible.
see here also: