If referring to software tuning, we've tried both and can say I'm very happy with the GIAC tunes we're been providing for M3s. The N54 flashes have been showing considerable gains have been very well-received in the e90 community.
GIAC will also be tuning our VF Supercharged M3:
More info can be found here:
http://www.m3post.com/forums/showthread.php?t=295845
Feel free to contact me directly if you should have any further questions.