とんでもないですって英語でなんて言うの？

Any of these sentence express the idea that it is OK that they have replied late.
You can also say things like 'no worries', 'it's alright', 'it's OK'.

"Don't worry about it" is a pretty standard response to a message like that.

If you are wanting to keep the nuance a little less casual, you can say a little more:
- I completely understand. Please don't worry about it.
- These things happen, please don't trouble yourself over it.
- It's not a problem at all, I completely understand.

Sometimes people apologise when there is no need to apologise and if that is the case then probably there is no need to make reference to it. In general in the UK, probably if you apologised for replying late, (as long as it was not so late as to be critical,) this would pass without further comment.
If the reason for the communication was to convey good news about something, you could say jokingly, "It's fine. The wait was worthwhile!" as the news is positive and what you wanted to hear.

Using the phrase "don't stress" or "don't worry," You are letting your teacher know that there is n need for him/her to be overly concerned about the late reply.

You can use any of these expressions.

You can easily use your own example, although, I personally would prefer the second sentence which I use frequently in my life.