Hello,
Here is the code for download and store files in document directory ios phone-gap app.

var fileTransfer = new FileTransfer();
fileTransfer.download(
uri,
filePath,
function(entry) {
alert("download complete: " + entry.toURL());
}
},
function(error) {
alert("download error source " + error.source);
alert("download error target " + error.target);
alert("download error code" + error.code);
},
false,
{
headers: {
"Authorization": "Basic dGVzdHVzZXJuYW1lOnRlc3RwYXNzd29yZA=="
}
}
);