The Glock 17 pistols is seen carried by Det. Mac Taylor (Gary Sinise) and Det. Danny Messer (Carmine Giovinazzo). Some of the uniformed NYPD Officers, as well as random crooks and other characters use Glock 17s as well.
Det. Donald Flack Jr. (Eddie Cahill) and some of the uniformed NYPD officers are seen using 2nd Generation Glock 19s as their main pistol in many episodes of the show (though sometimes they carry Glock 17s). Note that in real life, the Glock 19 is one of the sidearms of the NYPD.
Beretta 92FS
A blank-firing Beretta 92FS appears in "Fare Game" (S2E05), identified as the murder weapon.
Beretta 3032 Tomcat
In "All Access" (S2E21), what appears to be a Beretta 3032 Tomcat is pulled on Kid Rock.
SIG-Sauer P226
In "Manhattan Manhunt" (S2E07), Henry Darius (James Badge Dale) uses a SIG-Sauer P226 to hold Alexa Endecott (Peyton List) hostage. The SIG-Sauer P226 is also seen carried by DHS agents in "Charge of This Post" (S2E24).
SIG "Non Gun"
When Darius executes all of the prep school kids in Alexa's house, his P226 becomes a "Non Gun" SIG-Sauer replica (undoubtedly used because at the range of the shots, blanks would be too dangerous).
SIG-Sauer P228
A two-tone SIG-Sauer P228 is seen in "Stealing Home" (S2E20), which is stolen by an angry wife and kills her husband with it, using a .32 caliber round with a copper jacket, allowing the round to work in the 9x19mm handgun.
SIG-Sauer P229
Miami-Dade Police Department Lt. Horatio Caine (David Caruso) is seen with his SIG-Sauer P229 in "Manhattan Manhunt" (S2E07), this episode being a crossover with CSI: Miami.
Revolvers
Smith & Wesson Model 65
What appears to be a Smith & Wesson Model 65 is seen used at the beginning of "Live or Let Die" (S2E18).
Rifles
M16A1
In "Charge of This Post" (S2E24), Mac has a flashback to his days in the Marine Corps where he and many Marines are seen armed with M16A1 rifles with A2 style handguards.
M16A2
In "Heroes" (S2E23), U.S. Marines can be seen armed with M16A2's fitted with ACOG scopes during a tactical demonstration during Fleet Week, a few also being fitted with M203 grenade launchers.
In "Charge of This Post" (S2E24), a bomber named Dean Lessing (Eion Bailey) who was denied enlistment into the Marine Corps fires on the protagonists and holds a Homeland Security agent (Tembi Locke) at gunpoint with one before being talked into surrendering his weapon.
M40A1 Sniper Rifle
In "Heroes" (S2E23), an M40 sniper rifle is held by a Marine during Fleet Week.
Submachine Guns
Heckler & Koch MP5A3
Most N.Y.P.D. ESU officers can be seen using Heckler & Koch MP5A3 submachine guns, usually fitted with Surefire dedicated forend weaponlights.
Machine Guns
M249 SAW
In "Heroes" (S2E23), one of the Marines involved in the tactical demonstration can be seen armed with an M249 SAW.
Heavy Weapons
Cobray CM203 Launcher
In "Heroes" (S2E23), several U.S. Marines can be seen armed with M16A2 rifles fitted with Cobray CM203 Launchers (standing in for the M203) during a tactical demonstration during Fleet Week.
Mk 19 Grenade Launcher
Also visible at the Fleet Week celebration in "Heroes" is a Mk 19 grenade launcher, fitted to an M113 armored personnel carrier.