If you work long enough on Medicare policy, you'll hear what the difference is, but it's hard to find it written down anywhere.
With a new regulation, "Effective Date" is the date a policy is "effective" and "can be enforced." "Implementation Date" is a term of art that refers to the date by which CMS Part A, Part B contractors must have edits in place to enforce the policy.
Where is this written down? One place is the annual CMS report to Congress about its NCDs for the past year. Find the 2016 report here.
Example
For an example of the terms in use, see CMS Change Release 10878, which was (wait for it) issued on November 30, 2018, describing an NCD policy "effective" on March 16, 2018, and providing an "implementation date" of March 8, 2019.
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