What way is the best way to plum water to the whipple charger? Off the waterpump or will a thruhull with no pump be ok?

Use a transom mounted pickup and force feed it (no pump). Works great. Be sure to use a strainer if you boat in an area that has a lot of grass, seaweed, etc
Eddie

If you go the transom pickup route, you will want a pressure relief valve also.

Eddie, is there a need to put any relief valve on these if only hooking up to to a single intercooler from a smaller 3/4" npt transom pick up?

I run my transom P/U for the whipple with a strainer, but no check valve. Dustin Whipple said they are not necessary. No issues after 5 years.