1. Jets over Colts
2. Patriots over Rams
3. Giants over Patriots
4. Everything else
Jets over Colts was the equivalent of Boise State over the Rams, not the no-name Patriots over the Rams.
Before the Patriots Silenced The Rams, nobody acknowledged individual members on the Pats squad to the extent that Burress, Strahan, Youmenura (butchered spelling?), and (at least in a pedigree sense) Manning are acknowledged today. In that regard, the Giants over the Pats would not be nearly as shocking to "informed" footbally fans, but "as shocking" to the general population and to bookmakers.

I agree with this ranking. I really cannot understand anyone not picking Jets over Colts.

It's hard to imagine how anybody could be as shocked today by an upset as the fans of the time were shocked by the Jets' win. A few points:
1) There was no interleague play other than the Super Bowl. People widely considered the AFL to be a much inferior league and those impressions were massively reinforced by the results of Super Bowls I and II.
2) The Jets were only the third-best team in the AFL in 1968. The Chiefs and Raiders tied for that league's best record. Those teams were the AFL's first two Super Bowl representatives and they had gotten crushed. Why would the inexperienced Jets be expected to fare better than the AFL's two powerhouses?
3) To get to the Super Bowl, the Jets edged out the favored Raiders in an all-time classic game. The Raiders were driving for the winning score but they botched a lateral and then stood around thinking it was an incomplete pass allowing New York to recover it and move on. That win was the Jets' first postseason game EVER. Super Bowl III would be their second.
4) The Colts were a great team. They didn't just dominate in 1968, they had been a perennial contender for a decade. Only one NFL championship game between 1958-1968 did not feature either the Baltimore Colts or the Green Bay Packers. They were the two greatest NFL teams of the era. Many experts thought the 1968 Colts might be the best team ever to play.
5) I'm not sure the historic win made people see the Jets and the AFL in a different light, at least not immediately. It's kind of amazing if you read the
play-by-play of Super Bowl III. In the first half the Colts had drives to the Jets' 4 and 9 yard lines ended by bad interceptions, missed two FG's, and of course Earl Morrall famously missed a wide-open WR in the end zone on the half's final play. The Colts could have had a huge lead. The pressure created by the expectations might well have got to them. Their loss was probably seen as more of a fluke, at least until the Chiefs upset the Viking the next year.