I supposed it's possible for it to have been the Nicki, but since Ben had just put the kids to bed, she would have had to get out of bed and somehow beat Ben to Alicia's studio.
How is this supposed to work anyway? The puppet master's control weakens the further away he is to his victim. I remember an old story where he was trying to get Ben and Johnny to kill each other and had to follow them around NYC to maintain his control. I would think Alicia's control would fade away long before Lyja reached the Skrulls.