Both actually will round you out quite well. A lot of manufacturing companies are jumping on six sigma but are not fully behind the process. Becoming a six sigma certified black belt may help open some doors for you but I would bet that you will see come curtailment of six sigma programs in the next 5-10 years because of lack of upper management drive for it. Six sigma has a lot of great qualities and you can apply the concepts/methods to other areas of professional life (besides just improving the bottom line) when you can fully understand it.
The CQE will be easier to obtain, you just need to study for and pass the 5 hour exam. Six sigma certification will take you several months to complete and you will need to complete 1 or 2 six sigma projects to earn your certification. Also, you should have a company that will sponsor your certification. My certification cost $7,000 in 2002, plus travel and expenses for 5 weeks over a 6 month period. The CQE is much cheaper. Also, have you considered the P.E. license? The P.E. is as likely as the CQE to open doors for you but is more transferrable to other employment opportunities besides quality. When I changed professions in 2004, my P.E. helped me get the job, six sigma didn't mean anything.
