"Best way to remove nipples on water pump?"
The same way you remove them from people.
Twist em off.:D
Seriously though, it looks like you soaked them already and that's good.
Heat helps a lot (a propane torch is about as minimal as you can use, but does help)
Even though those have the cutouts for a tool those usually just strip out if the tubes have been in there for years.
Most end up having to use a pipe wrench, and even sometimes collapse the tube or break it off in the water pump doing it.
Our member @Rainy Day Auto made a tool that could work if they are not too rusted in there.
Start with the most non intrusive methods first and work you way up till you get them out.
