Buford has been GM for 8 drafts in San Antonio, but they have only held on to four first-round picks in that time: Beno Udrih, Ian Mahinmi, Tiago Splitter, and George Hill.
Nelson has been at Dallas the same amount of time, but only come away with 5 first rounders: B.J. Mullens, Maurice Ager, Devin Harris, Pavel Podkolzin, and Josh Howard.
It looks to me as if Petrie is the longest-tenured current GM (since 1994). Other guys who have over five years include (but might not be limited to):
Riley (Heat, 1996)
Paxson (Bulls, 2003)
Thorn (Nets, 2000)
Ainge (Celtics, 2003)
Buford (Spurs, 2002)
Nelson (Mavs, 2002)
Bird (Pacers, 2004)
Kupchak (Lakers, 2002)
Dumars (Pistons, 2000)
O'Connor (Jazz, 2000)
There's also Jordan, who has been with the Bobcats since 2004. I don't think he's technically the GM, but I get the feeling he's calling the shots.
So, at least 11 guys have been at the helm for 5 years (not counting Jordan).