For their whole bodies of work, it is hard to argue against Larry Beinfest, Brian Cashman, Theo Epstein and Andy MacPhail, as well as Walt Jocketty.
Beinfest has presided over the Marlins second WS title, and drafted well for them. He is now President of Baseball Operations and the Marlins do have a GM, but I am sure a lot of moves still come down from Beinfest. Cashman deserves recognition for his years with the Yanks and putting up with the Steinbrenners. Epstein took a solid Red Sox roster and built it into a winner. He's had some lapses in free agency, but he drafts very well and makes good trades.
Meanwhile, Andy MacPhail has a long list of work, laying the foundation for the Minnesota Twins over 20 years ago, and they still stick to what he put into place there for player development. Under his watch as President with the Cubs, they did draft well and saw success. The Orioles are a different story so far. Still, he deserves recognition for his work with the Twins for sure.
Walt Jocketty did some great work for the Cardinals for years, bringing in TLR, drafting Pujols and was with them for 13 years.
Today, I don't think anyone does more with less than Andrew Friedman. He's one of the best minds out there, and he has to be, because Friedman more than any GM needs to be worried about the future, as well as the present, when he makes any transaction. AA is certainly on his way up there, but I want to see the Jays make the playoffs before I crown him.
Frank Wren is probably my second. He had a failed term as the de facto GM of the Orioles, but has really done a great job with the Braves, and made some great trades to get value for the team.
I also want to point out Dan O'Dowd. I am glad that the Rockies gave him a chance to continue his work despite the Mike Hampton and Denny Neagle contract debacles. He's built a really good team up in Colorado and I think people tend to ignore them.