Muslims (and other Unitarians) frequently bring up John 17:3 as a polemic against orthodox Trinitarian Christianity. Because it has Jesus saying that the Father is the only true God, it must be denying that the Son is God they say.
And this is life eternal, that they might know thee the only true God, and Jesus Christ, whom thou hast sent. (John 17:3 KJV)
This would be a devastating verse if Christians were tri-theists and not trinitarians. If we believed that there were three Gods instead of one God, we could not confess that the Father was the only true God. However, because we are trinitarian, we say that the Father is the only true God, and the Son is the only true God, and the Spirit is the only true God. This can be seen in the Athanasian Creed, a Christian Creed from before Mohammed was even born.
Thus the Father is God,Athanasian Creed
the Son is God,
the Holy Spirit is God.
Yet there are not three gods;
there is but one God
The 2nd London Baptist Confession, of which I subscribe to, says the following:
In this divine and infinite Being there are three subsistences, the Father, the Word or Son, and Holy Spirit, of one substance, power, and eternity, each having the whole divine essence, yet the essence undivided: the Father is of none, neither begotten nor proceeding; the Son is eternally begotten of the Father; the Holy Spirit proceeding from the Father and the Son; all infinite, without beginning, therefore but one God, who is not to be divided in nature and being, but distinguished by several peculiar relative properties and personal relations; which doctrine of the Trinity is the foundation of all our communion with God, and comfortable dependence on Him.2nd London Baptist Confession of Faith Chapter 2 Paragraph 3
Biblically speaking, it is absurd to think that when John records Jesus’ prayer in John 17:3 he meant to communicate that Jesus was declaring Himself not to be God. John is very clear elsewhere that the Son is God and yet distinguished from the Father, as Trinitarians confess.
In the beginning was the Word, and the Word was with God, and the Word was God. The same was in the beginning with God. (John 1:1-2 KJV)
John shows that Word was both God and with God, showing He is both the one God and yet distinguishable from the Father before time began. He later lets us know that this Word is the one who became incarnate so we know he is referring to Jesus.
And the Word was made flesh, and dwelt among us, (and we beheld his glory, the glory as of the only begotten of the Father,) full of grace and truth. (John 1:14 KJV)
He also records Jesus declaring His Godhood:
Then said the Jews unto him, Thou art not yet fifty years old, and hast thou seen Abraham? Jesus said unto them, Verily, verily, I say unto you, Before Abraham was, I am. (John 8:57-58 KJV)
Jesus says He is ‘I am’, the name God gave to Moses in the Old Testament (Exodus 3:14). The play on the temporality of the verbs also indicates Jesus’ eternality. Abraham was, but Jesus is. The only one who can say He is is God Himself. So all John 17:3 proves is that Jesus is distinguishable from the Father (which Trinitarians whole-heartedly agree with). It does not prove that the Father is God to the exclusion of the Son.
A final note to Muslims. The rest of John 17:3 says it is not enough to know the Father, but you must know the Son who was sent as well. This is because the Son was the sacrifice for sins. One must believe in Him to have their sins atoned for and be credited with the righteousness by which we must be saved. You can read more about it here. I will leave you with one final verse from the Gospel of John:
He that believeth on the Son hath everlasting life: and he that believeth not the Son shall not see life; but the wrath of God abideth on him. (John 3:36 KJV)