We had a storm and water went under the crawlspace and submerged my heater 3/4 a way under water. Now it is not working. Is that covered by homeowners insurance?

Not unless you have flood insurance...

Each insurer and each policy is different. Read your policy or call your company.
HO insurers hate covering water damage from anything, even burst pipes, but especially storms, floods, and hurricanes.

You shouldn't have a heater in a crawlspace.