I might say something to the effect of I wish you well and you're in my thoughts.
Saying you're in my prayers, though it might sound wonderful to them, to me is being heartless. Like I'm saying nothing at all. Like saying something stupid like "I'll stomp my foot for you". Everybody knows stomping your foot isn't going to help a damn thing (unless they need help killing bugs). So saying you're going to do that doesn't comfort anybody.
And that's how I feel about promising prayers. I'm promising to do something that won't do a damn thing. To me, that's like an insult. Like telling a sick person you're not going to do anything for them.
Technically, thoughts doesn't do anything either. But knowing a person is cared for may comfort them. That's me saying that I do care and I'm thinking of them. Since I'm thinking of them, I'll probably follow up more. Which is comforting. Prayers are usually for the intercession of god - of somebody else to help them. Which ain't gonna happen.