Write x509 certificate into PEM formatted string in java?

This is not bad. Java doesn’t provide any functions to write PEM files. What you are doing is the correct way. Even KeyTool does the same thing,

BASE64Encoder encoder = new BASE64Encoder();
out.println(X509Factory.BEGIN_CERT);
encoder.encodeBuffer(cert.getEncoded(), out);
out.println(X509Factory.END_CERT);

If you use BouncyCastle, you can use PEMWriter class to write out X509 certificate in PEM.