"And this is eternal life, that they may know Thee, the only true God, and Jesus Christ whom Thou hast sent," (John 17:3, NASB).
First of all, it is not proper to make a theological doctrine out of one verse. Of this the Jehovah's Witnesses are sometimes guilty. Nevertheless, they do tend to take one or two verses on a subject and use them to interpret all the others. Instead of getting a balanced position, they arrive at an interpretation that is in agreement with their theological position. This is called "proof-texting" and is something the Jehovah's Witnesses do frequently.
Second, the context of Jesus' comment was that He was speaking as a man to His God. Remember, Jesus is both God and man, second person of the Trinity, the word made flesh (John 1:1,14). Since He was both divine and man, as a man He would naturally and properly say that His Father was the only True God. He was not denying His own divinity, but affirming the Trueness of God as was done in the OT: 'And now, O Lord our God, deliver us from his hand that all the kingdoms of the earth may know that Thou alone, Lord, art God,' (Isaiah 37:20). The truth is that Jesus was a man made under the Law (Gal. 4:4) and as a man He would be subject to God. Only in this case, Jesus was subject to the Father. That is why Jesus called the Father the only true God. But it is not a phrase that excludes Christ for Christ Himself said "Before Abraham was, I am," (John 8:58) and did not deny being called God by Thomas in John 20:28.
Third, John 17:3 must be examined in the light of the totality of scripture. We see that Jesus is called God in John 1:1,14; 8:58; 20:28; Col. 2:9; Heb. 1:8. Therefore, John 17:3 cannot be interpreted in a way that disagrees with other scriptures. Of course, some people simply state that John 17:3 cannot allow for Jesus being God. But the simple fact is that Jesus is called God by God and others. Therefore, the whole of scripture must be harmonized.