Perhaps the easiest ethical system to connect to a concept of immoral thoughts is virtue ethics. Under virtue ethics the core moral goal is to nurture a virtuous character. That is to train oneself "to notice, expect, value, feel, desire, choose, act, and react in certain characteristic ways." (quote source) The first six of these eight could reasonably be described as "inner thoughts".
Of course, virtue ethics is different enough from consequentialist or deontological models that things start to get a little blurry even using the same language. With the shift in focus from activities to agents, we should more properly say that a virtuous person has more of certain kinds of thoughts rather than categorising the thoughts themselves are right or wrong. Indeed, it's not even proper to tally up the thoughts except as some sort of inductive evidence of that training toward right character. A virtuous person wouldn't be someone who did or thought right vastly more than wrong over the last day or decade, but someone who placed in a situation to choose now would choose right.
Nevertheless, if we allow the sloppiness of talking of virtuous thoughts as being those which a virtuous mind entertains, there's room to say that thoughts of gratitude are better than thoughts of resentment, thoughts of reconciliation are better than thoughts of violence, careful evidenced reasoning is better than outbursts of prejudice, thoughts of respect are better than thoughts of lust or envy, and so on.
As always with virtue ethics, it interacts with the real world a step later. There is a virtue requirement to train ourselves toward conciliatory thoughts, because it increases our capacity to behave in a conciliatory way and to achieve mutually beneficial consequences. That's where consequentialist or deontological schools could fit in. A consequentialist might say a firefighter ought do press-ups in order to improve the probability of her achieving the consequence of rescuing people from the fire, or a deontologist might say it is the firefighter's duty to exercise to equip herself to do her duty in rescuing people from the fire. So likewise they might say she should prepare her mindset to be courageous, to prepare her value judgements to place rightly high value on other people, to apply herself to studying and rehearsing her trade, and in other ways to align her thoughts to better be able to do her duty or achieve good consequences.