If a user logs on to SQL Server management studio with a domain account, and the SQL Server database is installed on the same machine, then the NTLM authentication mode is always used. If a user logs on with a domain account, and connects to a SQL Server database on another machine, then Kerberos is used instead of NTLM. JDBC access should always be on a separate machine from the SQL database and use Kerberos authentication.
For more information, see the Choosing an Authentication Mode section in the Microsoft Tech Net website at: https://technet.microsoft.com/en-us/library/ms144284(v=sql.105).aspx.