Denver Seminary has put together a helpful bibliography on the major New Testament commentaries. Their suggestions for commentaries on the Gospel of John are listed below. (My comments are in blue)
Those marked with an * are particularly recommended by Denver Seminary
Keener, C. S. The Gospel of John: A Commentary, 2 vols. Peabody: Hendrickson, 2003.
*Köstenberger, A. John (BECNT). Grand Rapids: Baker.
Borchert, Gerald L. John, 2 vols (NAC). Nashville: Broadman & Holman, 1996-2002.
*Carson, D. A. The Gospel according to John (PNTC). G.R.: Eerdmans, 1991. (Carson is one of the best Evangelical commentators. He is a top notch academic who writes in a way that is extremely helpful for lay leaders and pastors alike. His work on John's Gospel is outstanding. If you can only purchase one commentary on John then get this one.
Kruse, C. G. The Gospel according to John (TNTC, rev.). Leicester: InterVarsity, 2004.
Morris, L. Commentary on the Gospel of John (NICNT). G.R.: Eerdmans, 1995.
Ridderbos, H. L. The Gospel of John. G.R.: Eerdmans, 1997.
*Burge, G. M. John (NIVAC). G.R.: Zondervan, 2000.
Witherington, B., III. John's Wisdom. Louisville: Westminster/John Knox, 1996.
Whitacre, R. A. John (NTC). Downers Grove, IL: InterVarsity, 1999.