There is no one "perfect" ship to explore with. You have to select the best, ie., most useful to you, unit that is available at the moment. If you have only discovered Map Making and the Trireme is the only ship available, its fruitless to speculate about the value of ageis cruisers vs. battleships vs. cruisers. You use the one that most closely fits your needs, and is available at the moment.
Personally, I much prefef to use a ship that can carry units to do my exploring because such a ship can carry a unit to pop huts and any unit that comes from said hut.
That said, I rarely built warships anymore because the trireme>caravel>transport line is all I need. 1: The AI should never be allowed to develop a strong navy. 2: in most games, the land masses are close enough together that you do not need a long ship chain to reach "accross the sea" to an AI trade city and when you get transports, your ships can usually end their turns in a port. 3: Napolean had the ideal way to defeat a sea power, ie., capture all his ports. its kinda hard for an opponent to support a navy if he has no coastal cities.
If you do have to deal with a strong naval power late in the game, a good battle group is a pair of battleships, 3 ageis cruisers, and a transport full of spies, perferrably all veteran units, especiallly the ships. The battleships can sink anything you run into, and the ageis cruisers will keep the air clear of insects.