[Update January 25th 2016: This is now an Abandoned theory as explained at the end of this post. March 8th Update: and now elaborated on here.]
Both popular favorites for the Crucifixion site today are within the city limits of modern Jerusalem but were outside New Testament era Jerusalem. The accounts all agree he was taken outside the City.
But given how much emphasis is placed on travel time in the accounts of his Burial and the women later coming to anoint him afterwards. I can't help but wonder if it was further then we think.
First I want to say that as far as Revelation 11 calling where the Two Witnesses bodies will lay the place where Jesus was Crucified. That city being where his execution was ordered still fits spiritually, as it is spiritually called Sodom and Egypt. But, at the same time this location being called where Jesus was crucified is my main argument against Jack Kelly saying the Revelation 11 Temple will be at the same place as Ezekiel's Temple (he believes that is Shiloh, I believe it's Bethel) so perhaps this is significant.
John 19:20 says he was Crucified "nigh to the city". But looking at other uses of the Greek word for Nigh, it's usually an idiom of time not distance. And in Luke 19:11 Jesus is refereed to as nigh to Jerusalem when he was at Jericho. And in John 11:18 Bethany is called "Nigh to Jerusalem". In some contexts it seems like it could mean "facing" or "on the way to". On the 14th of Nisan some people might have still been on the way to Jerusalem since the Pilgrimage command only required them to be there on the 15th. And that point of this detail of John is to explain why word of what was written on Jesus Cross spread quickly in Jerusalem.
Where do I think it was? Well I don't know for certain at all, this is just me throwing out that we should think about it.
But since my belief that Bethel is the site of Ezekiel's Temple has been relevant already, perhaps I should start there.
In Joshua 8:29 the King of Ai is hung on a Tree. Something I already talked about having possible typological relevance to the Crucifixion of Jesus. His body was taken down at sunset "even tide" which I recently pointed out being a relevant detail of Jesus Burial. The text can also be taken as implying he was hung west of Ai. Also west of Ai is Bethel, and I talked about how Abraham's altar was East of Bethel between it and Ai, and that Abraham's altar might be the site of Ezekiel's Brazen Altar. Putting all that together, this as the site of Jesus Crucifixion becomes compelling.
But the key word used in the text to identify where Jesus was crucified is Golgotha, The Place of the Skull. Garden Tomb proponents say this proves their site since it kind of looks like a Skull, but I don't think the Holy Spirit was going to make an identifier based on a Rorshach test.
The Hebrew word this name comes from is Gulgoleth, Strong number 1538. It's not used too often which can make it easy to research, but the majority of the time the KJV doesn't translate it Skull, though in my opinion not once is it a context where it totally lack grammatical sense to do so.
Only three places it's used could work to explain a location coming to carry that name, one involves tie ins with other passages to figure out how the Skull in question got to it's final resting place.
The least likely of these three to be relevant is Judges 9:53, where Abimelech's skull is crushed. I don't see that location coming to have that name.
But 2 Kings 9:34-37 is interesting. It refers to the fate of Jezebel, and her Skull and a few bones of her's being all that's left of her, and them being left there in the valley of Jezreel, which is also the valley overlooked by Meggido.
Now suggesting Jesus was Crucified there seems too far even for the logic I've argued already. And yet on the subject of Zechariah 12-14 and my considering it's relevance to the First Advent of Jesus. I talked about Chapter 12 verse 11 possibly being about the Mourning of Jesus, and it refers to the valley of Megiddon.
Third is Chronicles 10:10 which says the Skull of Saul was placed in the Temple to Dagon. The KJV translates this Head but a prior verse had used a different word for Head when describing his post-Morten decapitation. So I think this clearly tells us they removed the skin and meat from Saul's skull before placing it in there.
Then the men of Jabeshgiliead reclaimed the bodies of Saul and Johnathon and buried them in the Transjordan.
In 2 Samuel 21, seven descendants of Saul are Hung on Trees to appease the Gibeonites. In or near Gibea, Saul's former capital, in land allotted to Benjamin, his tribe. And this is dated to the beginning of the Barley Harvest, meaning near or at the time of Passover.
Later in verses 12-14 David had the bones of Saul and Johnathon moved from where they were buried to be reburied with these descendants of Saul in Zelah in the Sepulcher of Kish their father.
Jerusalem is also in Benjamite territory, but pretty close to the southern part of it. Given that Jericho which wasn't Benjamite territory was called nigh to Jerusalem, I think it's safe to say any place in Benjamin could be.
John 19:21 tells us the place where he was buried was right by the place he was Crucified. Yet we also know this Tomb was originally the tomb Joseph of Arimathea had prepared for himself. Arimathea is probably a Rama or Ramath of the Hebrew Bible. Joshua 18:25 and Nehemiah 11:33 places one in the territory of Benjamin, and Judges 19:13 and Isaiah 10:29 seems to place it near Gibea. Though Judges 4:5 places one near Bethel. That makes the place known as The Tombs of the Children of Israel an interesting place to look.
The Toldoth Yeshu drawing on various conflicting Talmud passages often speculated to be about Jesus, places the Crucifixion at a place called Lod/Lud/Lydda. In the Talmud this isn't said of a Yeshu at all but of Ben-Stada, I don't think Ben-Stada was Jesus, in fact I agree with the speculation that he may have been "That Egyptian" of Acts and Josephus. What is interesting here is that it seems he was likewise sentenced in Jerusalem then taken to Lud, which could perhaps imply this was a standard procedure.
The few references to Lod in the Hebrew Bible associate it with Benjamin (1 Chronicles 8:12; Ezra 2:33; Nehemiah 7:37; 11:35). Acts 9:32-38 has Peter perform miracles there, and calls it Nigh to Joppa but that is using the same word for Nigh again. So I saved this for last because it begins with something not only outside The Bible but ultimately hostile to it. However it can be seen as possible further evidence for it being in Benjamite land north of Jerusalem.
I'm going to add at the end here a bone for Preterists that they might find interesting. In the Talmud the "Slain of Lydda" refers to people killed in Lod by Rome during the Kitos War. The two notable ones were Jullian and Pappos. The Talmud also refers to a Pappos ben Yehuda, in one context implying a possible family connection to Yeshu and Mariam. Church history tells us unnamed grandsons of Jude the half brother of Jesus survived a persecution during the reign of Domitian, Eusebius adds however they were Martyred under Trajan, the Kitos War was under Trajan. Then a great grandson of Jude was the last Bishop of Jerusalem. Especially given a recent theory of mine, could Julian and Pappos be the grandsons of Jude? Which could then open up for preterists to consider that these two Martyrs of Lydda were the Two Witnesses Martyred where Jesus was Crucified in Revelation 11.
Interestingly an Islamic Hadith refers to Lod as being where the Dajjal will be slain. Many Islamic Antichrist proponents fixed on the Mahdi like to speculate that the Dajjal will be the Two Witnesses, independent of any of this.