let's think of a huge meteor that (was/were/is) near the Earth.
The intended meaning is that a huge meteor didn't exist before and let's have a thought experiment on what if a huge meteor were near the Earth. I think was or were would work for expressing the unreal situation.
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".
This sentence is talking about science. The context is not regarding whether it would happen in near future.
Or you can say this in this way:
"If there is a huge meteor near the Earth...."
In this sentence above, you definitely shouldn't use unreal situation, because you can't say that there isn't a huge meteor near the Earth right now. You don't know it is true or not, nor do you care.
In fact, you should use zero condition instead of unreal condition. See Grammar Lessons - Real and Unreal Conditional Sentences (If Clauses):
Form: If + Simple Present, + Simple Present
Use: The zero conditional is used to talk about things which are always true, scientific facts, general truths:
Examples:
If you cross an international date line, the time changes.
Phosphorus burns if you expose it to air.
If I wake up early, I go jogging.
NOTE: you can use "when" instead of "if".
