According to this GameFaqs post, Nathan and the Pirate are speaking in the Indonesian language. Using Google Translate, their conversation is roughly translated to:
Nate: Open the gate
Pirate: Who is this? Speak now!
Nate: Ah crap.
Nate: Damn you! Hurry up and open the door
Pirate: [undetermined swear word]1
1 This one is difficult to determine. Any translator is unable to give me a proper English equivalent, and only outputs the same text.
"Tai" more than likely translates to a swear word or another explicit phrase of some sort. Based on the Dake's Fortune script, "Tai" is used three other times by Eddy Raja in context of frustration or anger:
- Tai kamu (used twice, no proper translated)
- Tai kucing (used once, does translate to "damn you")