Could you please explain me a difference
The difference is due to 在 and 呢.

在 here is an adverb.
It means "in the process of doing something".

呢 is a modal particle.
Since you use period instead of the question mark, they are declarative sentences.
呢 indicates the notion that an action is in progress.
呢 also expresses the confirmation or emphasis on the facts.


他在吃饭呢。 What he is doing is eating meal.
This sentence indicates that the action of eating is in progress, and emphasizes the action.
他在吃饭。 He is eating meal.
This sentence simply shows that the action of eating is in progress.
It does not emphasize the action.
他吃饭呢。 He eats meal.
This sentence emphasizes the action of eating.
It does not indicate that the action is in progress.