When Unalaq merged with Vaatu was he in control or was Vaatu in control. Initially, it appeared that Unalaq was in indeed control as he was using his bending to fight Korra, going in and out of his Avatar State. However, later on in the fight, Vaatu forced himself out of Unalaq's mouth and ripped Raava out of Korra. After this Unalaq mutated and grew into a black larger version of himself with Vaatu's distinguishing features.
I don't think I could give a definite answer, but there are at least two points suggesting that Unalaq had control.
He attacked avatar Aang's statue
Why would he do that? Vaatu has little relation with Aang. Yes, Aang is the incarnation of the hero that defeated him, but chances are Vaatu doesn't even know this (he's been trapped for 10,000 years so he wouldn't know who Aang is) - or heck, he may not even care at all.
On the other hand, it is implied that Unalaq decided to attack Aang's statue to symbolise the end of the Avatar's era and proclaim himself as the new Avatar. As far as we know, Unoloq has better reasons to destroy Aang's memorial than Vaatu, so it was probably Unoloq the one who chose to do this.
He has proper movements to perform waterbending
Neither Vaatu nor Raava can bend elements. It is clear that Vaatu can waterbend since he fused with Unoloq, BUT observe his arms:
He is waving his arms in the same manner waterbenders do. The only one who knows how to do those moves is Unalaq, because this waving is waterbender (a.k.a human) knowledge.
And to top it all, it was not any sort of waterbending. He was doing the spirit thingy, and Unalaq is well-known for his mastery with that.
The thing is, there are also points suggesting Vaatu had control. For instance, the purple deathray thing is probably Vaatu's speciality. However using the deathray doesn't seem particularly difficult, so Unalaq might have just figured it out.