"Do you know of any material that lets capacitance through?"
Just avoid insulators!
Regarding the connection of a GPS to the iPad, I don't have on hands the technical details of the iPad (or iPhone) GPS, but on open water, it will surely be better that in an urban canyon. It can see a lot of sky --> a lot of satellite.
So, the internal GPS may be not so bad in your scenario.
But an external GPS with an active antenna will always be better (better GPS chip, better antenna and fewer electronics noise being far from the iPad radios).
You can find kits build by Microchip and Cypress for the connection of external devices to the iPod/iPhone, but you first, must enroll in Apple’s Made for iPod licensing program, by completing the online application at http://developer.apple.com/programs/ipod/.
Here is the microchip kit:
http://www.microchip.com/stellent/idcplg?IdcService=SS_GET_P...
And here's the Cypress one:
http://www.cypress.com/?rID=41030
Let me know if you need some advice on the GPS stuffs.