"is" is the 3rd person singular present tense of "to be"
"was" is 3rd person simple past of "to be"
Reading your sentences, I would put this interpretation on them:
I think this need some speech marks (")
Perhaps you are telling someone about something that happened in the past (you are using " thought", simple past of "think"). You had arranged to meet someone, and he didn't arrive at the specified time. You tell your friend later what you thought. I thought, "he is late".
Again, you are speaking about the past, but instead of using direct speech ("he is late") you are using indirect speech to say what you thought at the time.