I'm thinking of dualing a fighter to a cleric at level 3, giving me ** in one weapon and *** in another. I figure the *** should go to maces, but I'm a little tossed between putting the ** in hammers or flails (I figure one of those is a better bet, right). Any thoughts? Thanks.

Which game?

For IWD1, I would recommend flails for sure. My Ranger/Cleric has 2 stars in all three of these proficiencies, and I've hardly ever touched a warhammer. They do less damage than either flails or maces, and none of the ones I've come across in the game have particularly useful effects. I've found the selection of flails to be quite good, though, to the point where i hardly even use maces. That character spent most of the game with a +2 flail with a 15% stun chance, which was really nice, and I recently (in one of the expansions, can't remember which) switched to a +4 flail with a 10% stun chance and extra electrical damage.

I prefer maces, but maces and flails are both ok.

For me it depends what other weapons your characters are using.

I always have a character that can use a mace because there's an excellent mace you can buy in Lonelywood. However, I still use warhammers for 2 reasons, 1) fast attack speed means you can get a hit on the enemy before they can hit you and 2) weapon diversity, my characters almost always use different classes of melee weapons to avoid the problem of not having enough of one weapon type for 2 or more characters.

NotJabba is right in saying that warhammers tend not to have particularly useful effects. However, if you have a fighter type character that uses slashing or piercing weapons as a primary melee weapon, warhammers are a sufficient blunt damage backup. This leaves the maces and flails available for clerics.

TL:DR version

Maces and flails = best cleric melee weapons
Warhammers = backup blunt damage weapons for fighters.