The two married at St. Patrick's Old Cathedral in a Catholic ceremony attended by family and famous Hollywood pals, including Baldwin's "30 Rock" co-star Tina Fey, actress Mariska Hargitay, director Woody Allen, environmental lawyer Robert F. Kennedy Jr. and Baldwin's actor-brother, Stephen.
Thomas, 28, wore a silk Amsale gown with cap sleeves and a keyhole back neckline accented with crystal buttons. Baldwin's suit was designed by Tom Ford.
Hours before the ceremony, Baldwin took to his Twitter account, reciting lines from an Emily Dickenson poem. One read: "Was bridal e'er like this? A paradise, the host, And cherubim and seraphim The most familiar guest."
In the very next message, Baldwin posted a picture of his hand donning a simple wedding band.
The Associated Press contributed to this report.