There's actually what they call a seamans passport. It basically carries a travel document. They are used for crews to enter a country when needing to join a ship. Some country's allow you to enter visa exempt where you would normally need a visa.
They are not easy to obtain and have a strict criteria. They also don't give automatic visa free entry. You certainly couldn't use it as a holiday passport.
You say your delivering boats into Phuket? In that case, your certainly working in Thailand if your operating in Thai waters. Getting a tourist visa isn't going to solve that situation if it comes to light.
Unfortunately, other than extending his visa for another 30 days. There is nothing else for him other than leaving the country and buying a single entry tourist visa valid for 60 days in a near by country at an Embassy or consulate.
Be aware Monday May 14th is a Thai holiday. Royal ploughing ceremony. I'm not sure if that effects immigration offices, Embassys and consulates abroad.