Depends on how 'advanced' the systems are. A simple cast iron boiler (after being cleaned) might need some new electrical components and a new gas valve.

One full of microprocessors and other electronic is likely toast.

A contractor said both my hot water heater and furnace were shot when looking at dry-wall removal in my utility room.

They were each completely underwater.

Does anyone know the best course of action to take with water heaters and furnaces that were partially submerged?

I know the party line is to replace them if they've been at all under water. Some of ours lit up, but I'm not sure if that should be a vote of confidence.

Curious what people think. Likely will get a plumber to assess once they can actually be reached...