Well, which ship is best has been debated before in a few threads.
Since whats best is really going to vary from sailor to sailor it always ends up being a matter of whats most popular.
If anything it has been pretty much determined the most 'popular' ship is the War Frigate.
Personally I prefer the War Galleon as any 'perks' the War Frigate has over War Galleon I personally do not need for successful plundering. I find the larger hold allows me to stay out longer and get more plunder for my troubles. I generally have no problems filling the ship up and staying in the 'green' hull wise (usually 2-10 gold damage a trip). Additional hull strength, or broadside strength of War Frigate, I do not require.
As for gaining for reps, there is a Sailing reputation guide:
http://www.piratesonlineforums.com/f...ead.php?t=7141
It may help in deciding what targets are best, as it also depends on your own notoriety and sailing levels im pretty sure.
In the long run the higher the numbers, the better the reps (up to 100).
If your getting 100+ reps on a ship, its a high enough level
As for plunder, I find all the higher level 25+ War Galleons, War Frigates, and War Sloops all do somewhat the same, varying in amounts, and type. Alot of which I think is random, with a touch of "treasure sense" thrown into the equation. (Until reassignment of skill points comes about, i still think Treasure sense a waste of skill points, unless you anticipate using it to reassign your sailing as soon as it becomes available. As you progress, gold gets easier and easier to obtain.