I used Lincoln's commentary in my Gospel of John class this past semester and was very pleased with it.
I thought Andrew T. Lincoln in the Black's New Testament Commentary series would be preferrable for a semester-long course.
I really enjoy Köstebnberger's volume in the BECNT. For semester's read it's manageable, though he certainly doesn't skimp on the details. Köstebnberger is a leading Johannine scholar and I think is a leading voice in the field.