I don't think that he necessarily "loved" her more, but her relationship meant something different to him, and it was a different kind of love from his with Thomas.
When Flint lost Thomas, it was because they mutually loved each other and knew the consequence of their love. So, although Flint is part of the reason Thomas "died", he is not solely to blame because it was also Thomas'choice. With Miranda, she chooses to help Flint in obtaining Thomas'goal for Nassau, so her death still isn't fully Flint's fault either, but she wanted a peaceful resolution with England whereas Flint wanted to make England apologise to him for all they had suffered. If he had agreed to this peaceful resolution, she may not have died. She died while he gets to go on living, and he is ruined by the guilt of that.
On maybe a more important level, Flint and Miranda's relationship is exceptionally unique and complicated because of all they have gone through together. Flint was protecting Miranda by providing for her after what happened to her husband. Miranda was also Flint's sole confidant in the world, and the person who made him feel grounded and safe amongst all the madness of his life. She connected him to his old life before his piracy endeavours and served a way to remember Thomas.Their relationship was much more complicated because she was once his lover, was a friend and in ways, the only honest relationship in his life.
It just is a different type of grief with her, not more or less love.