Police said the crew reported at 9:14 p.m. that the men were involved in a shooting off the ship's stern.
When the ferry returned to New London from Block Island, officers boarded to investigate the scene.
Police say that Michael Richard, 53, of SC, was charged with carrying a firearm under the influence, carrying a firearm without a permit, reckless endangerment, and breach of peace among other charges.
Michael McMahon, 55, of Downes Road in Hamden, was charged with carrying a firearm while under the influence and breach of peace. The Coast Guard also responded to the incident.
Multiple witnesses, including off duty officers from other towns, pointed out who was involved in the incident.
Police said they seized a Glock 43 nine-millimeter gun.
Bond for both men was set at $10,000 and they are due in court on September 6. "Local law enforcement handled the situation expeditiously at the dock in New London".