GO PHILLIES!!! We use the minor leagues! Them Damn Yankees use their money! Not the minor leagues! They draft just to trade their players!
Um ... I think it's about equal (to drift off topic...). I count exactly four starting position players, two starting pitchers, and one ace reliever on each team that came up through the farm system:
YANKEES
Posada, Yankees' 24th round draft pick in 1990
Jeter, Yankees' 1st round draft pick in 1992
Cabrera, undrafted, signed by Yankees as an amateur free agent in 2001
Cano, undrafted, signed by Yankees as an amateur free agent in 2001
Pettitte, Yankees' 22nd round draft pick in 1990
Chamberlain, Yankees' 1st round draft pick in 2006
Rivera, undrafted, signed by Yankees as an amateur free agent in 1990
PHILLIES
Ruiz, undrafted, signed by Phillies as an amateur free agent in 1998
Howard, Phillies' 5th round draft pick in 2001
Utley, Phillies' 1st round draft pick in 2000
Rollins, Phillies' 2nd round draft pick in 1996
Hamels, Phillies' 1st round draft pick in 2002
Happ, Phillies' 3rd round draft pick in 2004
Madson, Phillies' 9th round draft pick in 1998
You could argue that among the starters listed here, the Yankees have several more who were undrafted free agents and the Phillies have more who were draft picks, but all except Chamberlain spent years in the Yankees farm system between being signed and debuting in New York, during which they could have burned out just like most draft picks tend to and during which the Yankees spent a lot of effort developing them; they're not in the same class regular free agents who already have proven major league records (like Texiera, Rodriguez, Lee, Martinez, etc).