nuge,
First off … welcome!
Good question and the guys above summed it up well.
One observation … back in the 60's about 70% of Cobras were 289 cars and the other 30% were 427s. Now about 50 years later and with thousands of Continuation / Replica / Tribute / Kit Cars out there. I would guess the vast majority (80 to 90%) are 427s. Given those numbers, one might conclude the 427 is the nicest shape, because that's what sells.
That being said, there does seem to be a renewed interest in the 289 cars, and there are more offerings in this part of the market than there were just a few years ago.
Since you asked, I think the 289 is the nicest Cobra shape. I am sure many here will respectfully disagree … and that's part of the fun. Truth is, they are both nice!