If someone says something to us, we don't reply in words rather we nod our head and in heart we say the words we could utter, such as Mr. X says to me "Good morning' but I don't reply saying "Good morning" rather, I just nod my head as if I am saying good morning in return__ in my heart there were words (good morning)... do we say, 'I said good morning to him in my heart'? or is there any other verb for this (for saying something in heart)?
I presume that "in your heart" is a standard phrase in your culture, but it does not really translate into English. The nearest equivalent would be silently, which means without speaking, or in the mind.
I silently returned his greeting.
The leader of the Daimler Chrysler group silently cursed himself for not thinking ahead of the trip. Shining Star - Pedro Vera, 2006
If by "in my heart" you mean that you communicated with him non-verbally (by nodding), then no. That's not how this phrase is used. It's meant to convey unexpressed feelings, not silent communication. Examples:
Although I never was able to see my friend during her illness to tell her I hoped she would get well, that wish for her was always in my heart.
Cyrano's unrequited passion for Roxanne was always in his heart, like a burning flame, frequently written but never spoken.