https://i.imgur.com/9JV1BTq.jpeg

As per picture, the Ship loading pumps are as close to the waterway as possible. Not sure what I'm doing wrong

The ship has to be in automatic and stopped at a station for the pumps to connect. For some reason, it's nearly impossible to make them line up by hand.

If, when you place the pump or hover over it, a yellow box appears around the waterway track section, then it ought to work. If not, then it might need to be closer or farther than you have it now.

Could increase https://wiki.factorio.com/Prototype/Pump#fluid_wagon_connector_alignment_tolerance, but it is on the pump, not the fluid wagon, sadly. Maybe just for the water pump?

I had forgotten that the ship-loading pump is actually a separate entity added in Cargo Ships. In fact, is OP using the vanilla pump instead? That might be why it's not connecting.

But both pumps can be used to interface with tankers, and both should work.

What is the point of having both, then?

Also, for me it was because it wouldn't connect on the left side of the ship. Only the right.

The 'ship loading pump' was removed in 0.2.0 and the regular pump can now also be placed in water (the placement restriction was why it was added in the first place). There shouldn't be any difference in loading on the left or right...