1966 NL Roberto Clemente over Sandy Koufax
Clemente (7.3 bWAR) had one of his better seasons for the Pirates in which he set career highs with 105 runs, 29 home runs, 119 RBI, and 342 total bases. He failed to lead the league in any major category, though, and Pittsburgh finished third in the standings. On the other side of the country, the Left Arm of God (9.9 bWAR, or another example of a season much better than Justin Verlander's) helped bring the Dodgers their third pennant in four seasons with what was arguably the best year of his career; he led both leagues in the pitching triple crown categories while also leading all hurlers in games started, complete games, shutouts, innings pitched, batters faced, and ERA+. Koufax, pitching through athritis that would force him into early retirement at the end of the season, took home his third Cy Young in four years and finished runner-up in the MVP voting for the second straight year. Consider that Koufax was unquestionably the best pitcher in all of baseball, whereas Clemente wasn't even the best position player in the National League that year because you could certainly make a case for Willie Mays, Ron Santo, Hank Aaron, and Dick Allen.
1964 NL Ken Boyer over everyone else
Boyer had long been one of the game's best two-way third baseman when he played 162 games and led all of baseball with 119 RBI for the eventual World Series champions in St. Louis. However, he didn't lead the league in anything else and he had plenty of help from slugger Bill White (finished third), offensive catalyst Lou Brock (tenth), NL hits leader Curt Flood (eleventh) and staff ace Bob Gibson (twenty-third), all of whom were just as instrumental to the Cardinals' success. The field was loaded with deserving candidates this year like Frank Robinson, Roberto Clemente, and Ron Santo, but none more so than the great Willie Mays (sixth). The Say Hey Kid piled up 10.2 bWAR while leading the league in home runs, slugging percentage, OPS, and OPS+. His numbers blow Boyer's out of the water, and he kept San Francisco in the pennant race for much of the year. If the Phillies hadn't disintegrated in September and coughed up the pennant, I think Boyer and runner-up Johnny Callison would have flip-flopped in the voting because the writers seemed to be relying on the standings when making their votes. In reality, it should have been Rookie of the Year Dick Allen (9.1 bWAR), not Callison, breathing down Boyer's neck. Like Jacoby Ellsbury of the Red Sox last year, Allen posted tremendous all-around numbers and did everything humanly possible to keep his team from blowing their late-season lead.
1962 NL Maury Wills over Willie Mays
Speedy shortstop Maury Wills (6.1 bWAR) sure could run, and he provided en exhilirating encore the year after Roger Maris surpassed the Babe by shattering Ty Cobb's single season stolen base record of 96 that had stood since World War I. As the leadoff hitter who played all 165 games that year, Wills accumulated some impressive counting stats and also led the league in triples. He had almost no power to speak of, though, resulting a very poor .373 slugging percentage (.074 ISO) and his 100 OPS+ indicate that he was nothing more than a league average hitter. He wasn't even the most valuable player on his team; Tommy Davis (6.8 bWAR) finished third, but enjoyed a much more dominant and productive offensive campaign by leading all of baseball with 230 hits, 153 RBI and a .346 batting average. On defense the line drive machine played all three outfield positions and spent 39 games at the hot corner as well. But all of that is moot, because Mays accrued 10.6 bWAR and led his Giants to their first Fall Classic since the franchise relocated to San Francisco. The Say Hey Kid led the bigs with 49 home runs and 382 total bases, and it's obvious that the writers voted more with their hearts than their heads this year.
1961 AL Roger Maris over Mickey Mantle
Basically the same argument from '62; voters let their judgment become clouded by the hoopla surrounding a broken record and overlooked the more deserving candidate. In a repeat of the 1960 vote, the M&M boys finished 1-2 in the MVP race with Maris edging Mantle by a whisker. Maris led the majors in longballs and RBI, but Mantle was better in every other way and his 11.9 bWAR dwarfed the single season home run king's 7.2. One of the most commonly cited statistics from this season is that Maris did not receive a single intentional walk that year because pitchers didn't want to put him on base for the Mick, which just goes to show how much pitchers feared the switch hitting slugger. While I'm at it, Detroit's Norm Cash (ten bWAR, .361/.487/.662 line) was also more deserving than Maris.
1960 NL Dick Groat over everyone else
Pittsburgh's light-hitting shortstop won the batting title, but didn't do much else with the stick as his meager two home runs, 50 RBI and .394 slugging percentage should tell you. Even though bWAR totals don't completely agree with me, I say Don Hoak (more productive in every offensive category except hits and batting average) and Roberto Clemente (same) were more valuable than Groat. There were plenty of deserving candidates in Willie Mays (9.7 bWAR), Ernie Banks (league leading 41 moon shots while playing shortstop everyday) and Ken Boyer (.932 OPS at the hot corner for the Cards), but two guys who really got shafted were a couple of Milwaukee Braves named Eddie Mathews (eight bWAR) and Hank Aaron (8.4) who finished tenth and eleventh, respectively, despite having the best all-around offensive numbers in the league. To give you some perspective on how fouled up this ballot was, Frank Robinson had as many bWAR as Groat and a 1.002 OPS, but finished 20th in the voting.