Jsa,
Fruit trees in general are prone to a ton of different types of diseases. This could be a rust or a scab or a viral something-or-other. I'm not sure if you realize it, but fruit trees need to be sprayed several times per year (as a gross generalization) - beginning just at bud break (when the leaf buds just start to crack open in spring) and then 7-10 days thereafter for 3 applications of fungicide. I'm certain the applications vary from fruit to fruit and maybe even variety to variety depending on what that particular variety might be more prone to (no sense in spraying for something a variety isn't likely to get). There has been a lot of advancements in organics - if you prefer that route- in recent years, so it's possible that you might be able to get what you need in organic.
My recommendation would be to look up what Honeycrisps are prone to and what the suggested treatments are, and then figure out which product you want to use to address it. But you have to be PROACTIVE - trying to treat after the disease shows up does not work. You have to spray in the spring, according to the directions to PREVENT the issue.
Thus, the only trees I have are peaches. They don't yield well, but I refuse to be a slave to the spraying requirements. It's unfortunate, but fruit trees are a LOT of work.
