Methanogens
Methane is a rather potent greenhouse gas -- it can trap over 100 times more heat than CO2 on a raw percentage basis. However, it's much shorter lived in the atmosphere, so you'll see varying comparisons about how a ton of methane compares to a ton of carbon dioxide for warming potential. (Hence why we mostly hear about CO2.)
But if you have a constant supply of methane, how short lived the effect isn't relevant. And since it's so effective at trapping heat, you don't need much of it to have an effect -- levels which are effective at warming the planet are far, far below those which have any combustion potential, and are also far below those which have any appreciable direct biological effect.
Methanogens are microorganism which produce methane. They're typically found in carbon rich, anaerobic environments ... such as marine sediments. On Earth they aren't the significant factor in global warming (at least aren't currently*), but for a fictitious ocean planet, one might hypothesize that they're much more active in converting the oceanic dead fall, and produce enough methane to warm up the planet significantly (especially when combined with the water vapor and carbon dioxide which is also in the atmosphere and doing their greenhouse thing).
*) Some researchers have proposed that at least one mass extinction might be blamed on climate change from methane-producing microorganisms.
You could also posit that there isn't a runaway greenhouse effect because your ocean planet has reached a stable equilibrium due to the particularities of your methanogens: as temperatures rise, your alien methanogens don't do quite so well, which reduces the amount of methane they produce. (Or warmer weather and more methane in the atmosphere results in growth of a different microorganism which eats the methane.) And since methane is removed from the atmosphere relatively quickly, things return to "normal" relatively quickly.
Note that if you want to get fancy, there are other compounds which could also work. CFCs and the like are also potent greenhouse gasses. For example, tetrafluoromethane is several thousands times better than CO2, and also sticks around much longer. So if there's a microorganism which produces tetrafluoromethane (or similar compounds) - even at a low levels - that can greatly contribute to warming.