I would personally stick with Manaphy. Cleffas can get donked by Tyrogue or even Zorua, and can be sniped or catchered easy as pie.
Running 1 Cleffa will not get you donked very often at all. As long as it wins you more games than it loses you it's a good card in the deck. And as far as snipe targets, you simply should NEVER play Cleffa down if you're not going to use the attack. Tyrogue is seeing a drop in play - there are more important cards to put into your deck now. Because if you're going first with a Collector and they open lone baby you're probably winning either way and his stalling capabilities are all but gone.
Not to mention once you've got an energy on manaphy, its attack is gaurunteed to work until it's KO'd, whereas Cleffa can stay asleep and screw you over if you needed to use EEK! again on turn 2, meanwhile while you're getting your stage 2 Vileplume set up your opponent might use a catcher and KO or damage something else.
If you're ever using these shuffle-draw attacks more than once during a game, you've already lost. That's two turns of potential prizes completely given up. Also if your deck gives you those kinds of hands twice in a row you should be considering re-working your list. The 25% chance excluding any switches or Catchers they play is slim enough it's more or less irrelevant. Besides, if you're immune and they don't kill you the prizes haven't changed at all so you're not a disadvantage. With Manaphy they can Catcher around it just as easily. You flat out should NOT be planning your game around a 60HP basic in the active position surviving to the next turn.
Also, if it's on the bench with very little damage, Manaphy can take a couple rounds of sniping before it is KO'd. I've run a Blastoise/Floatzel deck with two Manaphy and seem to start most games with manaphy active (you could even run a 3rd), so having to retreat and use Manaphy on the same turn is an uncommon situation.
With Catcher, Manaphy is basically as much of a free prize as Cleffa. If they're running Yanmega, only an inexperienced player will snipe the Cleffa right away anyway. Doing so only gives you an extra bench space and leaves more important parts of your setup unharmed. They will take the Cleffa as their last prize or when they truly have no other options and need to maintain the prize lead. If it's the latter, you probably win anyway. If you're running only 2 Manaphy and you usually open it, you're flat out lucky. With 4 Manaphy you should only be opening it around half the time. Besides, more than 1 Manaphy is overkill in any deck.
Not to mention, I usually get enough draw power from Supporters like PONT that I will end up with cards I need for the next turn and will not need to use Manaphy's Deep Sea Swirl on turn one. In those situations, it's nice to use Manaphy to just get in a quick 20 damage, 40 if you're up against something weak against water like Phanpy or Cyndaquil.
Using Manaphy for 20 damage is a luxury reserved for decks running a high count of Water energy. This deck and decks in general don't have that energy count. Also, Manaphy is an absolutely horrible attacker. You shouldn't ever be using the 20 damage attack. It's a wasted attachment.
I say stick with Manaphy, but its really up to you.
The deck that placed 2nd at worlds ran 6 30 HP Basics. The winning deck ran Cleffa. Pretty much every deck that cut ran Cleffa. You HAVE to listen to the best deck lists out there, because they're obviously doing something right. You're arguing against the results of one of the most respected tournaments of the year.
PS, I'm working on a Beartic/Vileplume deck as well. Good luck with it!
