It requires two teams to play a football game. Your secondary played marginally better than the Jets'. Henne completed 74% of his passes against your defense, 59% against the Jets'. The Dolphins converted 66% of their first downs against your defense, 46% against the Jets'.
The difference between the performance of the Miami passing attack in the games between the Jets and Patriots is explained by a difference in defensive philosophy and the difference in the level of play of Chad Henne (I think you would agree that players don't perform to the same level in every game). The Jets bring pressure and play tight coverage on the outside, with limited safety support. It results in rushed throws by opposing QBs, leading to a low completion %. It also results in big plays by the other team when the pressure doesn't get there, a high number of yards per completion. The Patriots play a soft coverage scheme, ceding the underneath stuff. Resulting in a higher completion %, but fewer yards per completion. In yards per attempt, the Jets allowed 8.3 YPA, the Patriots 7.7 YPA. That would be a small difference over the course of season, for a single game, it's almost nothing.
The Jets intercepted Henne once, the Patriots INT'd him three times. Two of Henne's INTs vs the Pats had nothing to do with the Pats coverage. The first INT was a terrible throw (short and behind his receiver, Marshall, directly into the arms of the Patriots' linebacker. Bad throws happen to everyone, there was no pressure on the play and a good throw would have resulted in a 20+ yard gain.) and the 3rd was a miscommunication with Marshall (again, no pressure, if they're on the same page, the result is a 4 yard completion). Neither of those plays had anything to do with the Patriots defense. Like I said before, the difference in the statistics is the result of a difference in defensive philosophy and Chad Henne's personal level of play.
Marshall had 5 catches for 50 yards, if that's what you consider shutting him down, OK. Maybe I've just been spoiled by Revis.
I didn't include Thigpen's numbers because the Jets didn't face Thigpen.