Ooh, I get to say this to someone other a fellow atheist: Remember, Christians have read the bible. There have been entire orginisations of people who literally spend their entire adult professional lives doing nothing but read the bible for two thousand years. If you think you've found the one Christianity Refuting Verse that they missed, no you haven't. In the same chapter, Jesus calls himself the Son of God, and claims to be one with the Father. Henceforth, simplified, the trinity- Jesus claims both to be a divine being and to not be The Heavenly Father, and there is one god, ergo "the Heavenly Father and the Son are both God, but not the same being". Now, obviously, I don't believe Jesus is God and neither do you, albeit for very different reasons. We both think you can show that he isn't. But if proving that was as simple as showing one bible verse, neither of us would be here because Christianity would never have got off the ground. They know about this verse, they've got defences of this verse, this debate has been going on since the first century AD. You're late to the party here.

Terminology

And this is eternal life, that they know you, the only true God, and Jesus Christ whom you have sent. (ESV)
αὕτη δέ ἐστιν ἡ αἰώνιος ζωή ἵνα γινώσκωσιν σὲ τὸν μόνον ἀληθινὸν θεὸν καὶ ὃν ἀπέστειλας Ἰησοῦν Χριστόν

The phrase the only true God, τὸν μόνον ἀληθινὸν θεὸν, is unique to the both the New Testament and the Greek Old Testament. An abbreviated form ὁ ἀληθινὸς θεὸς is used in one place:

And we know that the Son of God has come and has given us understanding, so that we may know him who is true; and we are in him who is true, in his Son Jesus Christ. He is the true God and eternal life. (1 John 5:20)

In the New Testament, true God is found only in the Gospel when Jesus speaks and John's letter.

The use in the LXX is also rare. Isaiah uses and repeats the most grammatically emphatic phrase τὸν θεὸν τὸν ἀληθινόν:

Which shall be blessed upon the earth; for they shall bless the true God, and they that swear upon the earth shall swear by the true God. For they shall forget the first affliction, and it shall not come up into their heart. (LXX-Isaiah 65:16)¹

Deuteronomy uses θεός ἀληθινὰ to describes His works:

God - his works are genuine, and all his ways are justice. A faithful god, and there is no injustice, a righteous and holy Lord. (LXX-Deuteronomy 32:4 NETS)

Chronicles has a prophet speaking to Asa of the true God. He uses θεῷ ἀληθινῷ:

¹ And Azarias son of Obed – a spirit of the Lord came upon him. ² And he went to meet Asa and all Ioudas and Benjamin and said, “Hear me, Asa and all Ioudas and Benjamin. The Lord is with you when you are with him, and if you seek him, he will be found to you, and if you abandon him, he will abandon you, ³ And for many days it has been for Israel without a true god and without a teaching priest and without law. ⁴ And he will return to the Lord, God of Israel, and he will be found to them. (LXX-2 Chronicles 15 NETS)

The omission of the article reflects the fact a genuine monotheistic expression is that of one God. In this case, the God and true God are identical terminologies.

As the LXX shows, a genuine monotheist knows there is only one God who by nature must be the true God. Even though ἀληθινός is unnecessary, on rare occasion God is called true God and even then the article is unnecessary. Nowhere does this phrase require additional qualification. The book of Isaiah ends with a picture of judgment and salvation before the new heaven and new earth. All people will bless and swear by the true God, τὸν θεὸν τὸν ἀληθινόν.

Clearly the terminology in the Gospel is unique and deviates from both the Old Testament and the similar phrase in First John:

μόνον
As evidenced by the LXX and John's Letter, the terminology to describe the true God does not require the additional term, μόνον. This raise questions. What reason does Jesus have to add this otherwise unnecessary term? Does μόνον have anything to do with Jesus referring to Himself in the third person? What reason does John have for changing what Jesus said by removing μόνον in the Letter?

The Fourth Gospel has many places where a key word has a dual meaning. For example, in His discussion with Nicodemus Jesus uses and repeats the term ἄνωθεν which means both again and above (cf. John 3:3, 7). This raises the question, does Jesus mean entrance to the kingdom of heaven requires being born again or being born from above?

Immediately before praying Jesus shows μόνον has another meaning:

³² Behold, the hour is coming, indeed it has come, when you will be scattered, each to his own home, and will leave me alone. Yet I am not alone, for the Father is with me. ³³ I have said these things to you, that in me you may have peace. In the world you will have tribulation. But take heart; I have overcome the world.” (John 16)

In English the sense of only in μόνον is one of separation: being alone, by himself. In addition to what Jesus says immediately before His prayer, 8 of the 10 uses of μόνον clearly mean alone, as in by himself. After feeding the 5,000 Jesus left the disciples and crowd; He went by Himself alone to the mountain (John 6:15). The next day the crowd realizes the disciples also departed; they had left alone (John 6:22). In the confrontation over the woman caught in adultery, after hearing Jesus' response the scribes and Pharisees leave one by one until Jesus is alone (John 8:9). The Father has not left Jesus alone (John 8:16, 29). A grain of wheat must die and remain alone to bear fruit (John 12:24).

Only in 5:44 is μόνον understood differently. Yet even here there are 14 translations which consider the sense of alone as proper:

How can you believe, when you receive glory from one another and do not seek the glory that comes from the only God? (John 5:44 ESV)
How can you believe when you accept glory from one another and do not seek the glory that comes from the one who alone is God? (John 5:44 NRSVA)

Conclusion
As there is no reason to add anything to true God, something additional is being conveyed. In the situation where Jesus prays to His Father in heaven, Jesus acknowledges His coming to earth left His Father by Himself, and so alone until He returns.

And this is eternal life, that they know you the God who is [at this moment] alone [by Himself] and Jesus Christ whom you have sent.

The meaning of alone agrees with Jesus' speaking of Himself in the third person and why John removes the word in the Letter. Once Jesus returns, the Father is no longer by Himself. Therefore, after the Resurrection, eternal life is found in He who is the true God.

The triune nature of God was affected first when the Son was sent and then when the Spirit was sent and remained on the Son. While praying in His human form He addresses His Father and states eternal life is found in the Father who is by Himself and Jesus Christ whom He sent and who is soon to be put to death. When He returns, He is in the bosom of the Father, who no longer is μόνον. The plurality inherent to the nature of God was restored; μόνον is no longer necessary so it can be said "He is the true God and eternal life."

1. Translation from R.R. Ottley, The Book of Isaiah According to the Septuagint (Codex Alexandrinus), Cambridge University Press, 1909, p. 321