I think, that as much as John has hurt Elena, he has known her for longer and loved her, her whole life. I think Alaric does care for Elena but not as much as John.
I'd say it's a difficult call to make, however that being said I think John still loved her more. After all he died for her knowing it was permanent, and the note he left for her spoke to that for me. I felt like that note had a lot of deep love coupled with regret in it, the kind of love only a parent can have for his own child. I mean, his family was indoctrinated for over a century to hate vampires and think they're inhuman abominations but when it was time to die that letter showed that while he wasn't necessarily over that indoctrination, he was willing to love her even despite that. I reckon it takes some powerful feelings of love to overcome those kinds of views.
Alaric and Elena are different, I think Alaric would die to defend her and Jeremy but I think he'd be more likely to risk his life for others than John was (although granted John was still a member of the council and in his mind a soldier that tried to protect others). I think after Jenna dies Alaric needs Elena and Jeremy as much as Elena and Jeremy need him, and that bond created by the fractured lives of both is strong, but at the end of the day I can't imagine it's quite the same as the love you have for your actual flesh and blood. Plus of course, John knew her from the moment she was born.
I think the love between Alaric and Elena is more of a love of equals, whereas the love between John and Elena was more John wanting to look after his daughter even if she didn't love him.
