You'd best consider the whole verse: "He who is least in the kingdom of heaven is greater than [John]."
I'm very well aware of the rest of the verse, thank you, but nothing in it cancels out the first part of the verse. Jesus was speaking of the end of the Old Covenant (of which John was the last prophet) and the beginning of the New Covenant. The Bible is full of passages explaining how the New Covenant is superior to the Old Covenant.