Grinding noises like you are describing sound like a failing transfer case.
There is a chain inside of the transfer case that can stretch and make a hell of a racket when it slaps against the housing or other parts.
Transmission problems mostly revolve around shifting issues, burnt fluid, vibrating torque converters, lost gears, things like that. If your problem is making odd noises, I would check out your transfer case first.
Water pumps are only a few components.
Housing, Impeller, Bearing, Shaft to connect the pully.
If your water pump’s bearing fails, it is very possible that it is causing your shaft/impeller to spin off balance, causing vibration/noise.