Both teams announced Thomas' death. The Mets said he died Monday morning in Pittsburgh. No cause was given.
Thomas played 16 seasons in the major leagues from 1951 to '66, the first eight for Pittsburgh, where he was born. He batted .266 overall with 286 home runs and 962 RBIs.
Nicknamed "The Original," Thomas made it to Citi Field in late August when the Mets held their first Old-Timers' Day in 28 years.
"This is my last fling for baseball," he said that day.
Primarily an outfielder and third baseman, Thomas was selected to National League All-Star teams in 1954, '55 and '58, when he set career bests with 35 homers, 109 RBIs and an .863 OPS. He finished fourth in the NL MVP race that year behind Hall of Fame sluggers Ernie Banks, Willie Mays and Hank Aaron, and just ahead of another player enshrined in Cooperstown: pitcher Warren Spahn.
Thomas was traded by the Pirates to Cincinnati in January 1959, and then to the Chicago Cubs and Milwaukee Braves. They sent him to the fledgling Mets in November 1961, and Thomas batted cleanup for New York in the franchise's first game on April 11, 1962, at St. Louis.
He finished that season with 34 homers and 94 RBIs, most in both categories by far for a lovable laughingstock team that lost a big league-record 120 games under Hall of Fame manager Casey Stengel.
Those numbers stood as the club record for home runs until 1975 and RBIs until 1970.
At age 93, he was a big hit on Old-Timers' Day at Citi Field last summer.
"I'm so thankful that my dad was able to go," Thomas' daughter, Maryanne Pacconi, said in a Mets statement. "It meant the world to him to see his old teammates. I was thrilled with how the fans greeted him. I was so happy to see him in uniform again. We will treasure those memories forever."
Thomas led the Pirates in home runs five times and RBIs four times, including his first year as a regular starter in 1953.
The team said he was a "proud family man and a man of great faith" who was "a valued member of the Pirates Alumni Association for over 30 years. He was most passionate about his charitable work with Camp Happy Days-Kids Kickin' Cancer, Courageous Kidz and the Millvale Meals On Wheels."
"Frank was proud to call the city of Pittsburgh home not only as a member of the Pirates but also as a person who spent his entire life here," team president Travis Williams said.
Thomas was preceded in death by his wife, Dolores, and daughter, Sharon. He is survived by his children Joanne Harrison, Patty Cain, Frankie Thomas, Peter Thomas, Maryanne Pacconi, Paul Thomas and Mark Thomas, the Pirates said.