Communicating with submarines is actually a nightmare. The saltwater ruins most radio communications, so you have no chance to receive GPS signals, which are pretty weak even on the surface.
One thing the military does/did to communicate with subs is use low-bandwidth text-only very low frequency radio, but you need colossal transmitters and there's no way the mother ship carries one. Hydrophones are also an option, and IIRC NATO even has a working sound-based modem to transmit digital signals to subs, but not sure if that has spread in the civilian market.
Military submarines also have a towed communications buoy that they can use to communicate with satellites. But that thing is connected to the submersible via a cable.
The important issue with VLF radio in this case is that what we need is sub->ship communication. VLF relies on massive antenna, often ground based to (very slowly) send message to subs. My understanding is that for comms the other way, the sub needs to raise an antenna above the surface (then possibly doing laser comms to a satellite so that no radio emissions give away sub locations).
One thing the military does/did to communicate with subs is use low-bandwidth text-only very low frequency radio, but you need colossal transmitters and there's no way the mother ship carries one. Hydrophones are also an option, and IIRC NATO even has a working sound-based modem to transmit digital signals to subs, but not sure if that has spread in the civilian market.