Deputy U.S. Marshal Marshall Mann (Frederick Weller) carries the full sized Glock 22 as his standard sidearm. His chief, US Marshal Stan MacQueen (Paul Ben-Victor), uses a G22 too.
Glock 23
Deputy U.S. Marshal Mary Shannon (Mary McCormack) has as her main carry weapon the Glock 23, which is the standard U.S. Marshal issue (as well as for the FBI and other agencies). In Season 1, Episode 2 (Hoosier Daddy), Shannon explicitly identifies her sidearm as a 'Glock 23'.
Glock 27
Mary's backup is the Glock 27 .40 which she has in an ankle holster. In Season 1, Episode 2 (Hoosier Daddy), she describes this explicitly as her "Glock 27" (as well as showing off her primary sidearm, her Glock 23). She uses this weapon when Spanky kidnaps her and no one sees the hidden weapon.
Taurus PT100 AFS
In "Hoosier Daddy" (S01E02), Luis Cruz (Steven Michael Quezada) pulls out a Stainless Taurus PT100 AFS pistol with gold accents during a drug negotiation gone bad.
Smith & Wesson 910S
In "Pilot" (S01E01), Frankie Santoro (Al Sapienza) uses a suppressed Smith & Wesson 910S. There is a continuity break in that the one he later carries in the room is a older Model 5906.
Smith & Wesson 5906
Frankie Santoro's (Al Sapienza) suppressed auto becomes a Smith & Wesson 5906 with old style fixed rear sights in the "Pilot" episode. In Season 1's "Trojan Horst" several assassins use 5906s with Novak sights.
Bryco M59
In "Pilot" (S01E01), Felicia Santoro (Kathrine Narducci) holds a Bryco M59 pistol in silver finish, until Marshal Shannon disarms her.
In "Trojan Horst" (S01E04), the assassin disguised as the 'wife' (D'Nette Pennington) uses a stainless Jericho 941 R Pistol.
Steyr SPP
In "Iris Doesn't Live Here Anymore" (S01E07), the street gang member uses a full-auto modified Steyr SPP pistol to kill the boyfriend's witness.
"Non Gun" Beretta
In "Good Cop, Dead Cop" (S01E09), Robert Eps (Jason Wiles) uses a "Non Gun" Beretta to threaten a corrupt cop in Chicago.
Revolver
"Non Gun" Revolver
In "Good Cop, Dead Cop" (S01E09), a "Non Gun" Revolver is pulled by a corrupt cop in Chicago.
Rifles
M4A1
In "Good Cop, Dead Cop" (S01E09), Albuquerque SWAT is seen armed with M4A1 Carbines.
Remington 700PSS
In "Hoosier Daddy" (S01E02), a Mexican Drug Cartel sniper uses a Remington Model 700PSS to try to assassinate a witness. The giveaway is the barrel tip and the bolt handle shape, which both indicate the Remington 700 Action, though one cannot determine the exact caliber (either .308 Win or .300 Win Mag) from a front view (the action length must be visible).