In the script of "Silent Enemy", this shuttle is described as "small" with its exterior referred to as a "dark form." The CGI model of the alien ship and its shuttle was made by Brandon MacDougall and can be seen at Doug Drexler's Drex Files. (X)(X) Early design sketches of the ship can be found at John Eaves' personal blog. 
The Star Trek Encyclopedia (4th ed., vol. 1, p. 441) identified this type of shuttle as a "Kovaalan shuttle". From the same source, it was stated this shuttle was carried aboard the Kovaalan starship.
Twenty-fifth century versions of this shuttle are encountered in Star Trek Online, where they are identified as Elachi Oschu-class shuttles.
As a 22nd century starship, this vessel was highly advanced in a technological regard, possessing strong shields and technology that prevented invasive scans from other vessels. It utilized a powerful energy weapon that fired green, crescent-shaped pulses. It had a crew of at least fifteen individuals, and carried at least one shuttlecraft. It also had the ability to emit a powerful dampening field, which could effectively disable an NX-class starship.
In the script for "Silent Enemy", this craft was described as "sleek and dark, so dark, in fact, that it's difficult to make out against the blackness of space." The CGI model of the alien ship and its shuttle was made by Brandon MacDougall. See Drex Files. (X)(X) Early design sketches of the ship can be found at John Eaves' personal blog. 
Several days later, the hostile vessel returned and attacked Enterprise NX-01, which had discovered the Axanar vessel and had sent a distress call from the ship.
During the encounter, the hostile vessel was more than a match against the Earth ship's spatial torpedoes. The hostile vessel quickly disabled Enterprise's warp drive and captured the small Earth ship in its tractor beam. The hostile ship proceeded to conduct a sub-molecular bioscan of the ship's crew, before locking onto the ship and beginning to drill into Enterprise's hull.
Before too much damage was done, Enterprise was rescued by an Axanar warship that first disabled the hostile alien's tractor beam, releasing Enterprise, before successfully destroying the ship in a one-sided fire fight. (ENT: "Fight or Flight")
This type of vessel wasn't identified in either the script for "Fight or Flight" nor the final version of that episode. In the script, the craft is referred to as "futuristic" and "highly advanced [...] with hull plating and conduits similar to the bio-pumps."
The fourth vessel (right), which was capable of planetary landing, was evacuating the planet when it suffered a rupture to its reactor casing while it was still in low orbit. The ship's captain requested permission to return to the surface after several of its compartments had flooded with radiation, causing injuries to several of the passengers and crew, including the AntaranHudak. The ship's request was denied; subsequently, assistance was rendered to the vessel by Enterprise. (ENT: "The Breach")
For information on transport #1, see VOY studio models; for transport #2, see DS9 studio models; and, for transport #3, see TNG studio models. Transport #4, the only one to be described in the final draft script of "The Breach", was scripted to be "large Alien Transport Vessel," marked with "some visible external damage." It appears to have been a new CGI model.