You can script from the action you do in the GUI. I didn't see this anywhere else (like any of the property functions), but this will do the job in script format:

USE [master]

GO

EXEC xp_instance_regwrite N'HKEY_LOCAL_MACHINE', N'Software\Microsoft\MSSQLServer\MSSQLServer', N'DefaultData', REG_SZ, N'D:\SQLdata\NewPath'

GO

EXEC xp_instance_regwrite N'HKEY_LOCAL_MACHINE', N'Software\Microsoft\MSSQLServer\MSSQLServer', N'DefaultLog', REG_SZ, N'E:\SQLlogs\NewPath'

GO