So I know that there are way to increase the crew quality after the fact via ship modifications, but are there rules for increasing the quality of the ship at ship creation? If so how much does it cost in SP?

Battlefleet Koronus has rules for component craftsmanship.

Core Book, pg 193 Section Titled "Constructing a Starship" 3rd point down:

"... All ships start with a competent crew... If the players wish to, they can gain an addition 5 Ship Points...by downgrading their Crew to Incompetent (20). Likewise, they can upgrade their crew to a Crack Crew (40) by spending 5... Ship Points. They may even upgrade their crew to a Veteran Crew (50) by spending 15 Ship Points."

Thank you, I knew it had to be in there somewhere..