Not even The Bible is Ho Yay free - see David and Jonathan for the boys and Ruth and Naomi for the girls. It says a lot that the dialogue between Ruth and Naomi is occasionally used at wedding services.
Oddly enough, the knee jerk hand wave to the former is it's Not What It Looks Like, meaning it apparently even looks like Ho Yay even to conservative Christians.
Marrying your gay lover's Sister is also a fairly common tactic.
Jesus was always surrounded by a dozen men all the time, and several counts of men kissing each other. True, that was the typical greeting at the time, but taken out of context:
Genesis 27:26- Then his father Isaac said to him, "Come here, my son, and kiss me."
This troper panicked and tried to describe the disciples thing as "They're Jesus' sidekicks. They're like Batman and Robin." Which only made my church youth director give me a look and say, "Are you sure you don't want to rephrase that? Find a different example, maybe?" Uh, oops.
John's gospel in some versions has him speak in third person. His name for himself? "The one Jesus/He loved." Now, sure, Jesus loves everyone, but when you give yourself the title of THE one he loved, maybe there's a little possessiveness there . . .
Ancient Greek had four different words for Love, so there's no reason for it to be ambiguous. If Wikipedia's excerpt is to be believed (I know, I know), the word the Greek gospels used was a form of "agape": Generally, a non-sexual, consuming obsession, insistent in the other's well-being without regards for how the lover is treated in return. Theologically (in Abrahamic circles), "agape" generally means "God/Christ cares for you no matter what you do". Out of context, though, especially considering there was very little Christian context before the Gospels and Letters, it could certainly be taken as "the one with whom Jesus was, like, totally infatuated, you'd have to see it to believe it".
And John the Evangelist was not John the Apostle. Unless he decided to make it some kind of self-insert fanfiction...
It needs to be noted that many women traveled with Jesus as well. The writers of the Gospels just didn't consider them important enough to warrant more than few mentions of them, and Mary Magdalene was the only one mentioned by name.
(Actually, there's Mary & Martha of Bethany, Mary the wife of Clopas, Joanna...to name but a few).
The Romans clearly read the subtext concerning early Christians - they took their custom of greeting each other with kisses regardless of gender or relation to indicate huge incestuous orgies by nightfall.
Apparently, according to Thomas Kyd, Christopher Marlowe shipped Jesus/St John...
Jesus also tells his new fisherman buddies that if they give up their jobs, he'll teach them how to catch men instead of fish - popularly translated as "I will make you fishers of men", but often translated as, literally, teaching them "to catch men instead of catching fish" (no word on the double-meaning of "catch)".
Jesus and Judas. The song 'The Garden' by P. J. Harvey seems to be about this particular pairing, or a least to invite them in describing two other characters...