Each persons favorite game will be their choice of best pin of all time. My favorite is LOTR so that is what I think would be best pin of all time.
Or you could rule out personal favorites and look to facts.
TAF has the record for highest selling pin or best selling pin of all time.
MM and TZ are pins that are usually in the number 1 spot on most top 100 lists that I've seen in the 20 years I've been collecting. Not sure which one has the longest running time in first place or most amount of time in first place.
So to sum it up. The best pin of all time would be one of these TAF, MM, or TZ.