Look, I'm not a big fan of these "greatest of all-time" scenarios in the first-place, so I'll give ESPN minimal credit here for at least keeping it to the last 50 years. Baseball hasn't changed that much like if you're trying to compare all those "Yankees buy the best player and keep winning" years.
My first hunch - which I guess you go with in life and trivia - is that the greatest one-year team of all-time is probably either the 1976 Reds or the 1984 Tigers, both perhaps not so coincidentally managed by the same guru, Sparky Anderson. I began watching MLB in June 1977, so the Big Red Machine's heyday is right before my viewing years. But as I was becoming more of a fan in 1979-82, those teams were spoken of with reverence, almost like you speak of Alabama football today or God.
When 81 told me they chose the Mets, my thought was, "Typical. They chose the geographically closest team to them, the same team that won the WS they claim was the greatest ever." But when you lived through it, I'm hard-pressed to say the 86 Mets were even the best team of the DECADE much less the best team of the last 50 years. Yes, they won 108 games.
They also played so poorly in the LCS that the MVP was the pitcher of the losing team, and two of their four wins over an upstart Houston team were in 12 and 16 innings. They couldn't beat Houston's starters to save their lives. Then they needed Boston to fall apart in both game 6 and 7 of the WS.
The Mets look better in retrospect because of what surrounds them as champions:
1981 - Dodgers in the strike year
1982 - Cardinals very quietly
1983 - Orioles very quietly
1984 - dominant Tigers
1985 - Royals come back from 3-1 down in both series
1986 - dominant Mets in regular season
1987 - 100 to 1 underdog Twins win
1988 - Dodgers upset both the A's and Mets
1989 - all anyone actually recalls is the earthquake, and that A's team was likely better than the Mets
The Mets and A's were the only pre-season favorites to really do it, although everyone expected Detroit to contend. But given the Tigers won the series in 5 and the A's swept, the fact the Mets had to go to 7 games always seems to me to put them in a bind.
Ask yourself this question: how many 1986 Mets could start on the 1976 Reds team?
1B - Tony Perez/Keith Hernandez
2B - Joe Morgan/Tim Teufel and Wally Backman
SS - Dave Concepcion/Rafael Santana
3B - Pete Rose/Howard Johnson
RF - Ken Griffey/Darryl Strawberry
CF - Cesar Geronimo/Lenny Dykstra
LF - George Foster/Mookie Wilson
C - Johnny Bench/Gary Carter
I mean, the only Met I can assure you would even start is Dykstra over Geronimo. I wouldn't take Strawberry over Griffey, either. (Folks think Griffey wasn't good - because his son was so great - but much like Barry Bonds takes the shine off Bobby, the Dad was a damn good player). Gary Carter was a VERY GOOD catcher, but he wasn't Johnny Bench. My goodness, the Reds on one team had the greatest catcher ever, the greatest second baseman, and the guy who got more hits than anyone else.
Now compare the pitching staffs:
1976 REDS
Don Gullett, Jack Billingham, Gary Nolan, Pat Zachry, Fred Norman, Will McEnany, Pedro Borbon Sr
1986 METS
Dwight Gooden, Ron Darling, Bob Ojeda, Jesse Orosco, Roger McDowell, Sid Fernandez, Rick Aguilera, Doug Sisk
Gooden as of 1986 was by FAR the best pitcher of all these listed. He also went 0-2 in the WS against Boston with an 8.00 ERA. Two of the three Sox wins came against Doc. Gullett probably would have been a HOFer if he could have stayed healthy. (He actually played for four straight World Champions - 75/76 Reds and 77/78 Yanks).
So tell me this...how could the Mets be the better team when AT MOST maybe four guys on their team would be able to play for the Reds? Aguilera 1986 was NOT the 90s Twins Aguilera, he was a nobody. I can see Gooden and Orosco from the pitching staff. At best.
And this is why I don't think they're the best team at all.