I had the great oppotunity to play both these courses back in the summer of 1998 during my "pilgrimage" to Scotland. It might be hard to pick one over the other...each offers a unique test of golf, filled with quirk and fun (as you stated above).
North Berwick was my FIRST EVER test of links golf, so it holds a special place in my heart. With the firth hard at your right as you play out, the course builds up in anticipation for the inward nine where you find the most "special" of holes, including the stretch from 13-17. Although the final hole is less than memorable it is still a great overall test of golf and a great walk to boot.
As for Prestwick, what can you say? Home to the first 13 Open Championships, the mistque, the quirk, the rail line. The first is a true butt-puckerer to try and find the fairway, and the course really never lets up from there with holes lie Cardinal, Himalayas, etc. Then on the inward nine you have the incredibly tough 10th, severe ground undulations, extremely tight fairways, bunkers the size of swimming pools (and just as deep!)...there is a little bit of everything out there.
Like I said...it would be hard to decide one over the other in a head-to-head match-up and you can't have much more fun on a golf course anywhere compared with these two places...let's just play 36 and call it a draw!