Installing Vapour Barrier in Crawlspace with Water Heater
I wouldn't. You'd essentially be sealing the heater's fate of rust and decay. (See what I did there?) 

First, you might find it less painful than you think to get the poly under the heater. A little levering or winching and it'll be off the ground the half inch you need. I'd put your main poly sheet down, then some thin plywood or something to protect it. 

You might even take this opportunity to do the annual drain and flush you surely do, making the unit lighter while you lift it.

Otherwise, just cut around the heater. The moisture that gets through that small area probably won't be a big deal.