isn't the same as traditional anti-virus or anti-spyware. From it's website: "Malwarebytes utilizes Malwarebytes powerful technology to detect and remove all traces of malware including worms, trojans, rootkits, rogues, dialers, spyware and more." It is not a replacement for traditional anti-virus or anti-spyware software. It is designed to be used along side those products without conflict and comes in a free or paid version. Malwarebytes : Malwarebytes Anti-Malware removes malware including viruses, spyware, worms and trojans, plus it protects your computer MSE
is Microsoft's full antimalware suite which helps protect against viruses, spyware, and other malicious software. It works well with Malwarebytes and I happen to use both. No problems at all.
As far as what's best, everybody has their own opinion. My opinion is the person using the computer will have the most influence on whether or not the machine gets infected. I'm sure others will jump in to try and convince you why their choice of product(s) is the best.