The Knights ideas are definitely stronger since they get +50% naval FL instead of +20%, +25% privateer efficiency (vs +15%) and they have +5% discipline from start.
However Cyprus gets cheaper and stronger galleys, faster claims (very nice), diprep, production efficiency and naval tradition decay.
I think it is a more balanced, diplomatic set. Another advantage of Cyprus is that they start in a better position to conquer the Holy Lands, plus they have a rich province.
You also have to consider that the Kinghts are a theocracy with also bonus PI in their ideas (so may be better staying catholic) while Cyprus is a feudal monarchy with all the bonuses this grants (PUs, HRE etc).
So both are very solid choices, depends on your playstyle really. I for one would go for Cyprus, since I already played the Knights and well I think that Cyprus has the best claims on reforming the kingdom of Jerusalem from an RP perspective, since it is a monarchy .