It depends on what one is looking for. There is no best course. An econometrics certificate programme should involve courses in statistics, regression analysis, time series analysis, statistical computing, mathematical methods, econometrics, statistical inference and probability. A programme involving these topics is good enough.
you can look up for the relevant courses in the NPTEL Online Certification list of courses available, these courses are offered by Different IIT's and IISC Bangalore, funded by MHRD, Government of India and the standards of these courses are extremely high. The Next session of these online courses will commence from 22nd January, 2018.
you can look into the website: nptel.ac.in for more details .
other than the above mentioned platform, you can also check the Edx website: (www.edx.org) for courses of your interest.
EDX offer a course using Eviews with IMF and acces to data base of World Bank. The name is "MFX: Macroeconometric Forecasting and you can obtain and certificate of achievement.
Coursera and INOMICS offer such courses. However, they would only constitute an introduction to econometrics and if you would like to enhance your understanding of the topic I would strongly recommend to study a relevant book (the books from Wooldridge or Gujarati would be good).