Is is often used similarly to "certainly". "He certainly is a tall person" or "he indeed is a tall person."
The difference is that, as someone mentioned, "indeed" is usually used to confirm what someone said previously. If my friend said to me, "my cousin is very tall," when I later saw the cousin, I would say "he is indeed very tall." If we were walking on the street and I saw a stranger, I would say, "he is certainly very tall," and my friend might look and say, "yes, he is indeed very tall." (He could say "certainly" here as well, but I would not say "indeed" in the first sentence; that would sound odd)