To me it's interesting to see different coding approaches from the different companies. From what was said in show seminars, it appears that at Stern there is a group discussion on direction, and then from there on it is pretty much up to a single coder/programmer for the main game code. At JJP, there seems to be a team approach from start to finish, with a lead coder but all the other coders contribute a lot, even Eric seems to get involved with advice. For the JJP deep code that has to be both good and probably a little difficult to coordinate, but they seem to be handling it just fine.
My point is that it seems like for Stern (and probably AP and Spooky also), you can pass judgement based on a game that their name is on. For JJP, there is a code team on each pin, so to judge JJP coders you would need to know which coder worked on which part of the code. Keith Johnson is their coding director and was also the lead on a few of their pins, but has a great supporting crew that work and grow on knowledge and technics together.
Short answer for the best coder (or coder team) to me is Lyman at Stern and Keith at JJP - that have coded the machines that I like the best - strictly code wise and nothing else.