“Is it time?” — Is something we’ve been waiting for happening now? Or, is something we know happens in general going to happen now?
“Is this the time?” — Can mean the same thing as above. Can also mean that you are wondering if now is the right time for something, or if another time is better.
“Is that the time?” — Refers to a specific, distant event (Example: “You always talk about my little sister getting chased by a goat.” Someone finds a picture of the sister with a goat. You can then ask, “Is this that time… when my sister got chased by a goat?”)