Based on the context of a thought experiment, and without editing any other part of your question, the correct choice is is.
"Were" can be thrown out because it is plural and wouldn't match the singular tense of "a huge meteor".
There is no "if" in this sentence or question words (what, which, when, etc.). Therefore, the noun-phrase that comes after "let's think of" is describing the exact situation you want the listener to imagine. Therefore using was here:
Let's think of a huge meteor that was near the Earth.
implies that there was a huge meteor near the Earth, but it is not near the Earth anymore. Since we want the listener to imagine a situation where the meteor is currently near the Earth, using is fits perfectly:
Let's think of a huge meteor that is near the Earth.
I will note that this is not the clearest way to say this if you intend to talk about how the conditions on Earth would change. It points towards just thinking about a meteor. (If you do intend to think about the meteor then disregard)
First if you want people to imagine an entirely new scenario (and not pull "examples" from their memory), a better phrase would be Imagine instead of "think":
Let's imagine that a huge meteor is near the Earth
By moving the "that", we instead are asking people to imagine a situation, rather than the actual "huge meteor". Compare "Imagine that a house is on fire" vs. "Imagine a house that is on fire".