In his head means he's thinking about you all the time which is good if you two are just starting out. In his heart would be basically a less committed way to say "I love you" which is good if you have been together a while but not if you are just starting out because that would be intense.
I have said both to people before and when I say your in my head it pretty much means I like you a lot, and I am constantly thinking about you. I want to spend time with you and I'm missing you when your not around. (a feeling that I get when I am in that early infatuation stage) When I say your in my heart I means I care about you, I consider your feelings as much as mine, and when your gone now, I don't just think about you and want you around. I actually feel a little bit of heartache. (a feeling that I get when I am in that mature love stage)
It depends on what context they meant it as and what was said before. They could be telling a person that they are thinking about them which is what I read it as but seeing as you haven't explained the situation it's a little hard to tell.
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