There's no single "best" endgame ship. Every class is built around a different way of playing, and the right one depends on what you actually enjoy doing in a fight, not just which has the biggest numbers on paper.
Tier 5-Upgraded and Tier 6 ships are both real endgame options, not a strict upgrade path from one to the other. Compared to the T6 version of an equivalent hull, a T5-U ship has the same Hull strength and the same number of console slots, but one fewer Bridge Officer ability, no Bridge Officer specialization seating, and no Starship Trait, all of which are exclusive to Tier 6. If you already have a T5-U ship you like flying, it's still viable; T6 is simply the ceiling above it, not a requirement.
Cruisers favor Hull strength and Engineering console slots over raw firepower, and they can often keep themselves alive without leaning heavily on outside help. If you'd rather stay in a fight indefinitely, absorb hits, and out-sustain the enemy than end things quickly, a Cruiser fits that instinct directly.
Escorts and Raptors get a Commander Tactical seat and the ability to run forward-facing Dual Cannons, trading Hull strength and durability for maneuverability and burst damage. If you'd rather end a fight quickly and rely on speed and positioning to avoid taking hits in the first place, rather than soaking them, this is that tradeoff made explicit.
Science Vessels get a Commander Science seat and can equip a Secondary Deflector, built around debuffing enemies and supporting a team rather than pure weapon damage. If you find yourself more interested in controlling a fight, or in the effects your abilities apply to the enemy, this is the class built around that.
A Battlecruiser gives up a Cruiser's Attract Fire ability (and sometimes a device slot) in exchange for Dual Cannon access, landing between a straight Cruiser and an Escort. If neither extreme quite fits, wanting some of a Cruiser's durability without fully giving up front-loaded damage, this is worth a look.
Carriers are endgame-exclusive and built around two hangar bays that launch fighters, shuttles, or other small craft to fight alongside you. If you like managing a small fleet instead of a single ship's own weapons doing all the work, this is a genuinely different way to play rather than a variation on the classes above.
A useful way to narrow it down: think back to a fight that went badly, and ask whether it was because you ran out of Hull before the enemy did, because you got hit too often to begin with, or because the fight just took too long and something eventually wore you down. Each answer points a different direction, more raw durability, more evasion and burst, or more crowd control and sustained pressure, which lines up with a Cruiser, an Escort, or a Science Vessel respectively.
Whatever you land on, plan it out in the Build Planner and record a real fight against it. A ship class points you toward a playstyle, but the same record-and-compare process from that guide is still how you confirm a specific ship is actually working for you.
New to the Build Planner? See Getting Started: Your First Build. More questions? See the FAQ.